OPUS Manual PDF

Spectroscopic Software
Version 4.2
Reference Manual
I 24333
© 2003 BRUKER OPTIK GmbH, Rudolf-Plank-Straße 27, D-76275 Ettlingen, www.bruker.de/optik
The text, figures, and programs have been worked out with the utmost care. However, we cannot
accept neither legal responsibility nor any liability for any incorrect statements which may remain, nor
their consequences. The following publication is protected by copyright. All rights reserved. No part
of this publication may be reproduced in any form by photocopy, microfilm or other procedures or
transmitted in a usable language for machines, in particular data processing systems without our written
authorization. The rights of reproduction through lectures, radio and television are also reserved. The
software and hardware descriptions referred to in this manual are in many cases registered trademarks
and as such are subject to legal requirements.
This manual is the original documentation for the OPUS spectroscopic software.
Table of Contents
1 Starting OPUS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
2 OPUS Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
2.1 Loading and Selecting a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2 OPUS Browser Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.3 Spectrum Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.4 Report Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.5 Datafile History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.6 3D Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.7 Selecting Frequency Limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.8 Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.9 Instrument Status Indicator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
3 File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
3.1 Load File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3.2 Unload File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.3 Undo Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.4 Save File (As) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.5 Sending a File by E-mail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.6 Exporting Data to GRAMS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.7 Exporting Data to InStep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.8 Deleting Data Blocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.9 External Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.10 VisualBasic Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.11 Load Data Point Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.12 Scan OPUS Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.13 Find OPUS Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3.14 Clone Entry and Clone Original . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.15 Add Comment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.16 RS 232 Communication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.17 Copy Data Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.18 Change Data Block Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.19 New and Open . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.20 Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.21 Print Preview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.22 Print Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
4 Edit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
4.1 Edit Parameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
4.2 Replay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.3 Information Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
iii
4.3.1 Editing Existing Information Blocks . . . . . . . . . . . . . . . . . . . . . . . 40
4.3.2 Creating a New File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
4.3.3 Displaying and Printing Information Blocks . . . . . . . . . . . . . . . . . 41
4.4 Creating an Information Mask . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
4.5 Structure Import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.6 Edit/Create Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
4.7 Attach Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
5 View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47
5.1 Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.2 Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
5.3 Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
6 Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
6.1 New Spectrum Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
6.2 New Report Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
6.3 New Registered Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
6.3.1 Text View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
6.4 Cascade and Tile Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
6.5 Arrange Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
7 Measure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57
7.1 Configuration of the Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
7.2 Measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
7.2.1 Basic Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
7.2.2 Advanced Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
7.2.3 Optics Parameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
7.2.4 Acquisition Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
7.2.5 Fourier Transformation Parameters . . . . . . . . . . . . . . . . . . . . . . . . 73
7.2.6 Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
7.2.7 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
7.2.8 Check Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
7.2.9 Error and Warning Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
7.2.10 Raman Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
7.3 Repeated Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
7.4 Rapid Scan - Time-Resolved Measurements . . . . . . . . . . . . . . . . . . . . . . . . 84
7.5 Interleaved Time Resolved Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . 88
7.6 Direct Command Entry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
7.7 Optics Diagnostic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
7.8 Temperature Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
8 Manipulate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .99
8.1 Baseline Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
8.2 Spectrum Subtraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
8.3 AB <-> TR Conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
8.4 Straight Line Generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
8.5 Spectrum Calculator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
iv
8.6 Cut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
8.7 Normalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
8.8 Make Compatible . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
8.9 Convert Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
8.9.1 Convert to Kubelka-Munk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
8.9.2 Convert to Reflectance Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . 116
8.9.3 Convert to ATR Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
8.9.4 Convert to Absorbance Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . 116
8.9.5 Logarithmize Reflectance Spectra . . . . . . . . . . . . . . . . . . . . . . . . 116
8.9.6 Convert Logarithmized Reflectance Spectra . . . . . . . . . . . . . . . . 116
8.9.7 Convert Single-Channel Spectra . . . . . . . . . . . . . . . . . . . . . . . . . 116
8.9.8 Convert Raman Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
8.9.9 Raman Laser Wave number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
8.10 Atmospheric Compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
8.10.1 Selecting spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
8.10.1.1Single-channel sample and single-channel refer-
ence spectrum in one file . . . . . . . . . . . . . . . . . . . . . . . . . 118
8.10.1.2Single-channel sample and single-channel refer-
ence spectrum in different files . . . . . . . . . . . . . . . . . . . . 119
8.10.2 H2O/CO2 Compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
8.10.3 Calculate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
8.10.4 Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
8.10.5 Limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
8.10.6 Atmospheric Compensation as part of the measurement process 121
8.11 Straylight Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
8.11.1 Selecting spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
8.11.2 Window material . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
8.11.3 Internal background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
8.11.4 Calculate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
8.11.5 Create new correction spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
8.11.6 Using straylight correction as part of the measurement process . 127
8.12 Noise generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
8.13 Moving Mean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
8.14 Make Monotone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
8.15 Smooth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
8.16 Derivative . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
8.17 Frequency Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
8.18 Raman Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
8.19 Black Body . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
8.20 Interferogram to Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
8.21 Inverse Fourier Transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
8.22 Post-Zerofilling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
8.23 Fourier Self Deconvolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
8.24 Symmetric Fourier Transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
8.25 Kramers-Kronig Transformation (KKT) . . . . . . . . . . . . . . . . . . . . . . . . . . 153
8.26 Extrapolation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
8.27 Abscissa Conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
8.28 Averaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
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8.29 Merging Spectra Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
9 Evaluate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .165
9.1 Curve Fit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
9.2 Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
9.3 Quant 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
9.3.1 Setup Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
9.3.2 Quant 1 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
9.4 Signal-to-Noise Ratio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
9.5 Peak Picking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
9.6 Quick Identity Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
9.7 Conformity Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
9.8 Quality-Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
9.9 Spectrum Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
9.9.1 Starting a Spectrum Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
9.9.2 The Search Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
9.10 NeuroDeveloper Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
10 Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .217
10.1 Forward, Back . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
10.2 Stacked . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
10.3 Scale All, Scale Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
10.4 Page Forward, Page Backward . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
10.5 Zoom In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
11 Print . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .219
11.1 Windows Default Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
11.1.1 Installing a Default Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
11.1.2 Selecting the Default Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
11.2 Defining Print Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
11.3 Print Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
11.4 Quick Print . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
11.5 New Layout – Plot Layout Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
11.5.1 The PLE Tool bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
11.5.2 The Pop-up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
11.5.3 PLE Page Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
11.5.4 Loading and displaying a spectrum . . . . . . . . . . . . . . . . . . . . . . . 231
11.5.5 The PLE Spectral Frame Properties . . . . . . . . . . . . . . . . . . . . . . . 233
11.5.6 The PLE Table Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
11.5.7 The PLE Text Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
11.6 Open Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
11.7 Print / Print Preview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
11.8 Print Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
12 Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .243
12.1 Script Recorded History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
vi
12.2 Macro Converter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
12.3 How to Run a Macro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
12.4 Debugging a Macro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
12.5 Macro Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
12.6 Compiling a Macro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
12.7 Adding a Macro to the Tool bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
13 Validation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .247
13.1 Instrument Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
13.1.1 Signal-to-Noise Ratio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
13.1.2 Test 100% Line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
13.1.3 Interferogram Peak Amplitude . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
13.1.4 Checking the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
13.1.5 x Axis Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
13.1.6 y Axis Reproducibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
13.2 Methods - Add Signature/Show History . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
14 Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .257
14.1 Logout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
14.2 Setup JCAMP/OPUS Conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
14.3 User Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
14.4 Change User Password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
14.5 Setup User Macro List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
14.6 Register OPUS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267
14.7 Customize Tool bars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268
14.8 Customize Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
14.9 Display Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
14.10 User Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
14.11 New Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
14.12 Save Workspace as . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
15 Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .277
15.1 Getting Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
15.2 Setting the Language . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
15.3 Rebooting the AQP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
15.4 Abort OPUS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .281
Data Block Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
Icons Used For OPUS Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
Additional Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
List of File Name Extensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
vii
1 Starting OPUS
Before starting the OPUS installation, read the attached documentation.
To install OPUS, insert the OPUS installation CD into your CD drive. Nor-
mally, the installation starts automatically. If the Windows Autostart option is
disabled, you have to start the installation manually by running the Setup pro-
gram from your CD. The installation program will guide you step by step. You
only need to follow the on-screen installation instructions shown in the different
dialog boxes.
At the end of the installation you will be asked to restart the computer. Note that
you need to restart your computer in order to complete the OPUS installation.
You may also be prompted to restart your computer when you install different
program components. In such a case do not restart until the OPUS setup has
been completed!
When the installation has been finished, an OPUS program icon is displayed in
the Windows Start menu. Click on this icon to start OPUS.
Figure 1: Windows Start Menu
The Login dialog box opens. Select your User ID from the drop-down list.
OPUS provides an independent user account system which regulates the access.
If you use OPUS for the first time, the User ID drop-down list includes two pre-
defined user records Default and Administrator. Select either one of them.
Bruker Optik GmbH OPUS Reference Manual 1

Starting OPUS
Enter OPUS in the Password entry field. Use capital letters, as the password is
case sensitive. Once you have assigned yourself a user record in OPUS, it is
possible to determine your own User ID and Password.
Figure 2: OPUS Login Dialog
OPUS includes different accounts for operator and administrator rights. Users
defined as Operator have limited access rights compared to users defined as
Administrator. The rights depend on the User ID selected.
The Assigned Workspaces identify the user interface and access right. You can
always select those workspaces from the drop-down list which have been
defined for your User ID. When you use OPUS for the first time, we recom-
mend not to change the standard Default workspace.
Click on the Login button and the About OPUS window opens.
2 OPUS Reference Manual Bruker Optik GmbH

It shows the serial number of your OPUS copy and the registered user name.
The basic OPUS package integrates these additional licensed packages as an
all-in-one application.
Figure 3: About OPUS Dialog
Click on OK to open the OPUS user interface. The interface appearance

depends on your screen settings and the operating system you use. Thus, the
screen display of the following dialog boxes may not show exactly the screen
contents displayed on your screen. BRUKER recommends a minimum graphic
resolution of 800 x 600 pixel and true color.

Starting OPUS
(a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
Figure 4: OPUS User Interface
The OPUS user interface header shows the type and status of the operator cur-
rently logged in.
(a) The pull-down menus can be used to access all OPUS functions.
(b) The icon bars may be configured to quickly access frequently-used functions.
(c) The browser window of the OPUS file manager, similar to the Windows Explorer.
(d) The spectrum window for full views and zoom operations.
(e) The overview window always displays the full frequency range of the selected data files.
(f) A context sensitive online help.
(g) The status bar indicating background tasks.
(h) Instrument status (see section 2.9):
Green = OK
Yellow = Warning
Red = Error
All settings (menus or icons) are individually configurable and will be reloaded
when you start OPUS next time.

2 OPUS Basics
This chapter introduces the basic OPUS functions and provides general infor-
mation on OPUS windows and the processing of data files. The OPUS functions
for data acquisition and manipulation are described in detail according to their
order on the pull-down menu.
OPUS dialog boxes are similar to those of Windows. If you have already gained
experience in working with Windows, it will be easy for you to use OPUS.
OPUS supports drag & drop as well as shortcuts, e.g. copy (STRG+C), cut
(STRG+X) and paste (STRG+V).
To use these shortcuts, you first have to select the text or file you want to pro-
cess. Drag & drop simplifies the copy and paste process, but can only be applied
on files. In this case click on the files icon in the OPUS browser and press the
left mouse button, while moving the file to the dialog box (or window) you want
to use. If you release the mouse button, the file will automatically be loaded into
the dialog box selected.
Dialog boxes often consist of several tabs. Click on these tabs to change
between them. Buttons and menu items are only active, if they are displayed in
black. Grayed buttons are not available.
Figure 5: Example of a Dialog Box with Two Tabs

OPUS Basics
2.1 Loading and Selecting a File
Load Spectrum Dialog Box

If you load a file, either
• use the Load File command from the File menu,

• click on the icon in the tool bar or
• drag the file from the Windows Explorer into the spectrum window,
OPUS browser or any OPUS dialog box.
If you select the file you want to use, the Load Spectrum dialog box displays the
following features:
(a) (b) (c) (d) (e) (f) (g)
(h) (i) (j) (k)

Figure 6: Load Spectrum - Active Preview
a) The title bar shows the directory in which the file is stored.
b) The drop-down list includes directory paths to search for spectra files.
c) Using this arrow you can return to the last selection.
d) This icon allows to return to the parent directory.
e) Using this icon you can create a new directory.
f) Various options to display the file list.
g) The preview window displays a small spectrum range without indicating the axes. Data
blocks are displayed on top of the preview window. They include additional information
on the spectrum file.
h) File list of the path selected.
i) You can also manually type the name of the file you want to load into this entry field.

Loading and Selecting a File
j) It is also possible to load spectra of different formats, e.g. JCAMP-DX or GRAMS.SPC

files. These files will automatically be converted into the OPUS file format.
k) Parameters are additional information appended to the OPUS file. Sometimes not all
parameters to be selected by each drop-down list will be defined for each spectrum file.
This means that some parameter fields may remain empty.
You can select several spectra in the spectra list using the STRG or Shift key
while selecting the spectra. In this case the number of selected files will be
shown instead of the data blocks and spectra previews. Clicking on the Open
button will load the spectrum into OPUS and automatically close the Load box.
Select Files Option

You will encounter the Select Files option in various dialog boxes. Figure 7
shows an example of the Select Files tab in the Baseline Correction window.
Figure 7: Example of Select Files Option
Select Files tabs include File(s) to... fields. Spectra files to be processed can be
entered into these fields. You can either drag and drop spectra files displayed in
the OPUS browser window or Windows Explorer. If you select the spectra files
before opening the Select Files tab, or if you double click on the file data block
in the OPUS browser window, the spectra files will be automatically displayed
in the specified entry field.
There are functions which cannot be used for all types of data. It is not possible,
e.g. to apply an AB<->TR Conversion to an interferogram. Sometimes, the
parameters of an OPUS function have to be set prior to loading a file, in order
to be able to select the file. If selected data blocks can principally be processed
by OPUS functions but the parameters do not match the data, the file name in
the File(s) to... field will be indicated in red and a warning symbol displayed
(see Fig. 8).

OPUS Basics
Figure 8: Convert Spectra – Parameter Mismatch
To remove data blocks from the File(s) to... field, select the data block and use
the Delete key on your keyboard. If you press the Shift or STRG key, you can
select several files in one File(s) to... field.
2.2 OPUS Browser Window
The design and functionality of the OPUS browser is similar to the Windows
Explorer. When loading an OPUS file the file name, data blocks and file status
information are displayed in the browser window. If you position the cursor on
the file name, a small text field pops up indicating the complete data path. If you
place the cursor on a data block, the text field shows the operator name, sample
name and sample form.
(a) (b) (c)

Figure 9: Browser File List
a) If you have opened several spectrum windows you can switch between them
using the display icon. If you click on the sign, the file name display will be
minimized.
b) The blue document symbol indicates that the file has not yet been manipulated.
The number next to the file name indicates the number of copies made of the file
loaded. You can load a file several times into the OPUS browser window.

OPUS Browser Window
c) The small icon bar underneath the file name represents data blocks which are
part of the spectrum file. The data blocks displayed in Fig. 9 indicate a transmis-
sion spectrum, single channel spectrum, interferogram and single-channel back-
ground spectrum. If the data block symbols are colored, this indicates that
spectra or interferograms are displayed within the spectrum window. Use the left
mouse button to select one data block. If you press the STRG key, you can select
more than one data block. Selected data blocks are always indicated by a red
frame.
The possibilities to select files are similar to those using the Load File option or
Windows Explorer.
If you select one file using the left

mouse button, press the Shift (⇑)
key and click on a second file
again. All the files between these
two files will also be selected.
Additionally selected by using

STRG
Figure 10: Select files
This kind of file selection causes the files to be automatically registered for pro-
cessing functions. If you have changed or added files using a processing func-
tion, the blue document symbol will be hidden by a red one. If you have loaded
the same spectrum several times, the copies will be incremented.
If you right click on a file name, a pop-up menu opens.
Figure 11: Pop-Up Menu for File Manipulation
As changes made to a file are not automatically saved in the file directory, you
have to store these changes using the Save File option. Unload File means that
the file is removed from the spectrum window, but is still available in the file
directory. If you have modified the file using a processing function, you can
Undo all Manipulations. The Show Parameters option displays all information

OPUS Basics
on data acquisition which have been saved to the file. For details on parameters
and information data blocks, see chapter 4.
The Copy Entry and Clone Original options are used to duplicate spectrum
files. The difference between these two options is that Copy Entry copies a data
file which has been manipulated, e.g. if a baseline correction has been per-
formed. The Clone Original option copies the original spectrum file.
If you right click on a data block, the following menu pops up.
File has been

loaded twice
Figure 12: Pop-Up Menu for Spectrum Manipulation
Using this menu you can change the layout of spectra within the spectrum win-
dow. Apart from changing the color you can zoom selected spectra ranges.
Almost similar to this pop-up menu is the one displayed when you right click
into the spectrum window. The options will be described in the next section.

Spectrum Window
2.3 Spectrum Window
The spectrum window and overview window are on the right side of the OPUS
user interface. When you have loaded a file all spectra and interferograms
included in this file will be displayed.
The default settings for the spectral range are from 4,000 to 400 wave numbers
and from 0 to 1.5 extinction units. However, you can scale the spectrum to show
the complete data range. Use the Scale all command in the Display menu or
click on the icon. If a file consists of more than one data block, only the
first data block is displayed in the spectrum window.
In Figure 13 the Scale all command has not been used. Therefore, only the over-
view window shows the total spectral range of data. The part shown in the spec-
trum window is depicted on a white background, while the remaining data range
is grayed out. If you position the cursor on the gray area, the cursor will change
its form from to . Now you can move the borders of the spectral range
(white) displayed in the spectrum window pressing the left mouse button.
Spectrum Window
Lock Window Size
Overview
Figure 13: Spectrum and Overview Window Showing Lock Button

OPUS Basics
If you position the cursor between overview and spectrum window, the cursor
changes to . This allows you to re-size the windows. You can disable this
function using the Lock button, which becomes visible if you right click on the
this boundary.
If you right click on a spectrum within the spectrum window, a pop-up menu
will be displayed (Fig 14). This menu allows you to change the spectrum color,
to zoom a specific spectral range or to shift the complete spectrum.
Figure 14: Pop-up Menu within the Spectrum Window
To magnify a part of the spectrum window, select the Zoom In option from the
pop-up menu. A crosshair is displayed in the spectrum window. Click on the left
mouse button to draw a frame around the spectral range you want to magnify. If
you click on the left mouse button a second time, the crosshair cursor disappears
and you can reposition the frame. Now, left-click again and the spectral range
selected will be resized to the spectrum window. Use the Zoom Out command to
decrease the magnification or the Scale all Spectra option and go back to the
original view by selecting Show Everything (XY) from the pop-up menu. The
Page back option in the Display menu allows you to have the last 10 spectral
ranges displayed again. For details on scaled spectra display, see chapter 10.
The Shift Curve command includes different options. The first allows to either
shift the Whole Curve vertically or to stretch the curve to the Top or Bottom in
y direction. Select the relevant option and shift the curve. Click on the spectrum
and press the left mouse button. If several spectra are displayed, you can shift
each one of them using the Shift Curve option. Deactivate the Shift mode by
right clicking. To undo these changes, select Reset from the Shift Curve option.
The Crosshair command also includes different options. If you select Cursor, a
the cursor is displayed as crosshair. To follow the data points of a spectrum, use
the Follow Data option. This option allows to display the current crosshair posi-
tion (e.g. wavelenght or absorption unit) in the upper right corner of the spec-

Spectrum Window
trum window. You can comfortably read out the x/y positions directly from the
spectrum. If you right click, the cursor changes into its regular form.
You can change the spectrum color and remove it from the spectrum window by
selecting the Change Color and Remove from Display options.
Use the Add Annotation command to identify peaks even more precisely. Right
click on the spectrum and select Add Annotation from the pop-up menu. At the
cursor position an arrow is inserted indicating the wave number of this data
point, by default. To edit the annotation text, right click on the wave number
and select Properties from the menu which pops up. If you position the cursor
onto the arrowhead and click on the left mouse button, you can move the arrow-
head.
Add Region facilitates the selection of frequency ranges when using QUANT
methods.
Copy and Copy All as well as Paste can be used to copy files between different
spectrum windows. Special sections which have been copied can also be added
to different programs.
Properties opens the Display Settings dialog box.
Display Settings
Figure 15: Display Settings – Display Limits
Use the Display Limits tab to change the size of the displayed region.

OPUS Basics
Figure 16: Display Settings – Axes
The Axes tab allows to depict each spectrum with additional axes on top and on
the right side of the spectrum window. If the spectrum window includes more
than one spectrum and the spectra are displayed in stacked mode, you can
define separate axes for each spectrum if you select X between.
Figure 17: Display Settings – General

Report Window
General allows to change the background color and the default height of the
overview window.
You can open more than one spectrum window by selecting the New Spectrum
Window option from the Window menu. You can either tile or stack windows.
Tiled windows are convenient to copy data between spectrum windows.
Stacked windows are displayed separately. You can copy one spectrum from
one window to another if you select the relevant spectrum. Or you drag & drop
the spectrum from the OPUS browser window to one specific spectrum win-
dow.
2.4 Report Window
You can use the report window to display numerical or text information, e.g. to
display measurement parameters or evaluation results. This kind of information
is stored in report blocks. Double click on such a report block (except for peak
tables) to open a report window. A blank report window can be opened from the
Window menu (see chapter 6.3).
Figure 18: Report Window

OPUS Basics
The information included in the report block is displayed in form of a directory

tree on the left. If you select one item in the directory tree, the specific data are
displayed on the right. Click on the column title to sort the column data. For
report blocks which include headers, a three-column window is opened and dis-
plays both the header and data matrix.
Right click on a report window and select Properties from the pop-up menu.
The View Properties dialog box opens. You can activate the Header preferred
checkbox and specify the font and font size if you click on the Printer Font but-
ton.
Figure 19: Report Window - View Properties
2.5 Datafile History
A special type of report window is Datafile History. Any manipulation made in

the spectrum and even in the measurement parameters are recorded in a non-
editable, non-deletable history datafile. Figure 20 shows a Datafile History,
including several spectrum manipulations.
The first line of the datafile history states the operator as well as the OPUS ver-
sion and the name of the spectrum. Then, all manipulations and their parameters
are listed in the order of their performance.
All pieces of information are saved in a data block ( ) together with the
processed spectrum in one spectrum file. This ensures that all data manipula-
tions can be reproduced, as every kind of manipulation as well as the operator
name are automatically recorded.

3D Window
History Datafile history History list

data block
Figure 20: Report Window Showing the Datafile History
2.6 3D Window
3D windows can be used to plot contour graphics. These windows are part of
the OPUS MAP package and described in detail in the OPUS MAP manual.
2.7 Selecting Frequency Limits
In case of some OPUS functions you need to define frequency limits first to be
able to process a data file. You have got three possibilities to select a frequency
range:
• Select the frequency range interactively.

• Apply the current frequency limits of the spectrum window by click-
ing on the Get Display Limits button.
• Enter the limits manually.

OPUS Basics
If you want to interactively select the frequency range, load the spectra you
want to process and click on the Interactive button in the Frequency Range tab.
Figure 21: Frequency Range Selection
The Select Frequency Range(s) window opens which displays the loaded spec-
tra. Depending on the x-startpoint and x-endpoint defined (see figure 21), the
spectra will either exactly fit the window or a larger frequency range will be dis-
played. In the latter case the area which does not contain any data is displayed in
gray. If you see a gray window without any data at all, you have to select the
window again and define different values for the x-startpoint and x-endpoint.

Selecting Frequency Limits
Figure 22: Selecting Frequency Range Interactively – Moving the Left Frequency
If you position the cursor on the boundary between the white and gray area, the
cursor changes into a double arrow. Press the left mouse button and move the
cursor to either the left or right side.
To define several frequency ranges right click on the gray area and select Add
Regions from the pop-up menu. Within the white section the cursor changes to a
cross arrow. If you press the left mouse button, you can move the entire fre-
quency range selected.

OPUS Basics
Figure 23: Choosing File Limits Interactively – Defining the Endpoints
If you click on the OK button, you confirm the limits of the frequency range to
be used for data processing.
2.8 Toolbars
OPUS provides toolbars which can be individually configured to quickly access

frequently used functions. Next to each icon and within the status bar context-
sensitive tooltips pop up when you position the cursor over that icon.
Figure 24: OPUS Toolbar Showing a Tooltip
A double click on the icon instantly carries out the associated function. The
icons are also displayed next to their respective function in the pull-down
menus.
You can customize the various tool bars to best suit your personal requirements.
The tool bar configurations are stored together with your workspace settings in
one file which has the extension .ows. OPUS default settings are stored in the
DEFAULT.OWS workspace. For details on tool bar configurations, see section
5.1 and 14.3. For a icons list, see Appendix.
Instrument Status Indicator
2.9 Instrument Status Indicator
The instrument status is shown at the right end of the status bar (see Fig. 4). A
green status light indicates that the instrument is OK. When the instrument sta-
tus indicator turns yellow, it indicates a warning, if e.g. the instrument test has
to be repeated. A red instrument status light indicates a severe error, e.g. if a
spectrometer component is defective. The instrument status is stored in a mea-
sured spectrum. If you click on the instrument status light, a diagnosis dialog
pops up including additional information on the status and specific help.
Options for the diagnosis can be set up using the User Settings options in the
Setup menu.

OPUS Basics

Load File
3 File
The File menu includes all features necessary for your data file management.
Apart from basic functions such as loading, saving, printing and exporting the
File menu allows to start VisualBasic scripts and external software programs.
Using the Exit command you can close OPUS. .
Figure 25: File Menu
3.1 Load File
The Load File command has already been described in section 2.1.

File
3.2 Unload File
The Unload File command removes files from the OPUS browser and spectrum
windows. However, when unloading files they will not be deleted from your
hard disk. The Unload dialog box only consists only of the Select Files tab (see
section 2.1).
3.3 Undo Changes
Use this command to undo all changes made in a data file since it has last been
saved. The original data will be restored. The History report, however, will not
be reset.
3.4 Save File (As)
The commands Save File and Save File As differ in the options available to
store files. Save File consists only of the Select Files tab. Enter all files to be
saved into the File(s) to Save entry field. The Save File As command is also
used to export data from OPUS.
If you use the Save File As command, the Select Files tab allows you to define
spectral data to be stored, and the file path. Use the Change Path button to
browse the directory of your hard disk. If you activate the Overwrite checkbox,
already existing files will be replaced by new files. This option cannot be acti-
vated when working in GLP mode. It is also possible to increment file names.
For details, see section 14.10.

Save File (As)
Figure 26: Save Spectrum
On the Mode tab you can set the parameters for exporting OPUS data in a file
format used by third party software like GRAMS1 or InStep2; in addition, two
ASCII formats, Data Point Table and JCAMP.DX, are available.
Optional you can move the original file, save all data blocks of the file and auto-
matically remove all copies of the file by checking the respective boxes.
1. GRAMS is a registered trademark of Galactic Industries Corporation, 395 Main Street, Salem, NH 03079-9891.
2. InStep is a registered trademark of Infometrix Inc., 2200 Sixth Avenue, Suite 833, Seattle, WA 98121.

File
Figure 27: Save Spectrum – Mode
In case you selected the Data Point Table format the third tab will become
accessible. Enter the format of the table and the separator; alternatively choose
Separator is TAB to use tabulator signs. In Figure 28 the resulting table will
consist of a ten digit number with five digits before the decimal. Y only restricts
the output to the intensity values.
In addition, you can limit the file size to 64 KB by checking the Max. 64 KB
box.
Figure 28: Save Spectrum – Data Point Table

Sending a File by E-mail
3.5 Sending a File by E-mail
You can also send your OPUS files by e-mail. On Windows this requires at least
MS Service Pack 3.
After you loaded the OPUS file into the Browser send them using the Send File
command. If you check the radio button Whole File the complete file content
will be sent, even if only part of the file information is loaded in the spectrum
window.
Figure 29: Send File
When you click on the send button the data will be transferred to the Windows
mail software as an attachment. You can specify an address and include a com-
ment. However, if you are using mail for the first time you will have to config-
ure it.
3.6 Exporting Data to GRAMS
You can also export the data acquired with OPUS to GRAMS (via Dynamic
Data Exchange) for data processing. The procedure is very much the same as
described in the last section, only that you use the Send File to GRAMS com-
mand. Before transferring data you will have to start GRAMS.

File
3.7 Exporting Data to InStep
In a similar manner, data can be exported to InStep using the Send File to InStep
command.
3.8 Deleting Data Blocks
As you have seen before OPUS files usually consist of several data blocks.
These can also be deleted individually from the file (not only removed from
the display!) using the Delete Data Block command. All corresponding data of
a deleted data block, like search tables and integration results, will also be lost!
In GLP mode, restrictions apply.
3.9 External Program
You can start third party software and your own programs from the OPUS user
interface using the External Program command. Details are given in the “OPUS
Programming” manual.
3.10 VisualBasic Scripts
You also can start VisualBasic scripts from the OPUS user interface using the
VisualBasic Script command. Details are given in the “OPUS Programming”
manual.
3.11 Load Data Point Table
If you have spectral data in the form of an ASCII table you can import it into
OPUS. Compared to the usual Load File dialog you have to specify the column
(i.e. which column holds the frequency x and which the intensities y), the num-
ber of data points to import, and the point with which to start. Also, you have to
indicate the type of spectrum.
3.12 Scan OPUS Files
OPUS comes with a powerful tool, the Find OPUS Files command, to perform
search runs on the spectra you have stored on your hard disk. Find OPUS Files
searches a data base for text strings defined by the user. Before you can use the
Find OPUS Files command for the first time, you have to build this database.

Scan OPUS Files
This is done with the Scan OPUS Files command. From the dialog box select
the drives you would like to scan. You should select all drives that contain spec-
tra. Click on the Scan Files button to start the scan. Depending on the amount of
spectra building the database and the size of the drives this will take several
minutes. While this process is active, “Scan OPUS Files” will be displayed in
the Status Bar.
Figure 30: Scan OPUS Files – Path to Scan
On the second tab of the dialog box you can limit the information stored in the
data base by indicating the OPUS parameters you want to include or exclude.
Excluding OPUS parameters reduces the size of the database. The Add Path and
Delete Path buttons are inactive and reserved for future use.

File
Figure 31: Scan OPUS Files – Parameter Evaluation
3.13 Find OPUS Files
As soon as a database has been generated you can search for file names, text
strings in files or file parameters. In case you added spectra to your hard drive
since you generated the database, it is recommended to update it by clicking
Update Database now prior to a search run. The time of the last update is dis-
played to the left of this button.
Enter the string to be searched in the Find Text in Fields line. You can specify
whether to find exact matches only, any of the words, or all of the words you
entered. You can further restrict the search by specifying a date in the Find in
Period frame. Select between after, before or between these dates to narrow
down your search. Start the query by clicking on Find in Database.
All matching spectra are displayed in a list. When the cursor points on a spec-
trum, the selected parameters and information from the info block is displayed
in the table on the right. Select files from the list and load them by clicking on
Load Selected Files.

Clone Entry and Clone Original
Figure 32: Scan OPUS Files
3.14 Clone Entry and Clone Original
Clone Entry and Clone Original are used to duplicate spectrum files. Use Clone
Entry to make a copy of a data file that has been manipulated, as for example
background corrected. Clone Original creates a copy of the original data of such
a file.
3.15 Add Comment
Add Comment opens a box where you can add a comment to a spectrum. This
comment will appear in the Report Display under Datafile History.
3.16 RS 232 Communication
RS 232 is a function which allows you to communicate with external devices

via the serial port(s) of your PC (COM 1, COM 2, etc.).
The function is available from the File menu. In general the function is intended
to be used in a macro or VB-Script rather than using it interactive. The interac-
tive mode can be used for testing the communication.

File
Write/Read Functions
After calling the function interactively the following dialog is shown:
(a) (g)
(b) (h)
(c) (i)
(j)
(d)
(e)
(k)
(f)
(l) (m) (n)
Figure 33: RS 232 Configuration - Write/Read
(a) This checkbox enables or disables the Write function

(b) The status of the write function is shown here (i.e. Writing..., Timeout etc.)
(c) Here you can enter the text line(s) which shall be written to the external device.
If you enter more than one line each line will be optionally terminated with the
specified line terminator
(d) This frame is used to specify the line terminator. Carriage Return (CR) and Line
Feed (LF) are already predefined. If you need a different terminator check the
"Other" radio button and enter the ASCII code of the terminator in the entry
field aside the radio button. If you choose "None" no terminator will be sent.
(e) This frame is used to specify the terminator which is sent after the last entered
character. Choose either "None" if no terminator should be sent or "Other". In
the latter case you must enter the ASCII code of the terminator in the entry field
aside the radio button.
(f) A click on the "Write" button sends the text entered in field B. If the "Read"
function is enabled the read function is automatically started to read the answer
from the external device.
(g) This checkbox enables or disables the Read function.
(h) The status of the read function is shown (i.e. Reading..., Timeout etc.)

RS 232 Communication
(i) The answer read from the external device is shown in this area.
(j) This frame is used to specify the terminator for the read function. Whenever this
terminator is detected the read function will stop. Carriage Return (CR) and
Line Feed (LF) are already predefined. If you need a different terminator check
the "Other" radio button and enter the ASCII code of the terminator in the entry
field aside the radio button. If you choose "None" the read function will wait for
answers until the time out is reached.
(k) User the "Read" button to activate the read function only.
(l) Exit from the function and store the current settings. No write or read activity is
started.
(m) Exit from the dialog without saving the current settings
(n) Show the online help.
Interface Configuration
The second tab of the dialog allows to set the different options for the serial
interface:
(g)
(a)
(h)
(b) (i)
(c)
(d)
(e)
(f)
Figure 34: RS 232 Configuration - Settings
(a) All currently available serial interfaces are shown in the combo box. If a serial
interface is not available (e.g. a mouse is connected to COM 1) this interface
will not be offered in the combo box.
(b) The current settings of the interface are shown in this area.
(c) Enter an appropriate timeout value in milliseconds.

File
(d) This checkbox enables the option to configure the interface with a "Mode"
string. You find details about the Mode command in the documentation of the
operating system. If the box is not checked the controls E and F are not visible.
(e) Enter the mode string to be used for configuration (without specifying the serial
port)
(f) A click on this button sets the current settings according to the mode string. The
settings will be shown in B
(g) The "Restore Default" button reads the current settings which have been speci-
fied in the operating system as default.
(h) The "Change Settings" button calls the setup dialog of the operating system
which is described below.
(i) The button "Store as Default" overwrites the operating system settings with the
current settings.
Change Settings Dialog

The following system dialog is shown after clicking on the "Change Settings"
button:
Figure 35: RS 232 Configuration - Settings
This dialog can be used to specify the following communication parameters.

• Baud Rate
• Data Bits
• Parity
• Stop Bits
• Handshake
The same dialog is shown when the parameters of the serial interface are set up
from the operating system "System Settings" function.

Copy Data Block
3.17 Copy Data Block
Single data blocks may be copied from one OPUS file into another Tis is only
possible with certain block types, e.g. INFO.
Figure 36: Copy Data Block
The data blocks to copy are entered into the upper box, e.g. by dragging from
the browser. The lower box shows the destination of the blocks to copy.
3.18 Change Data Block Type
Changing the data block type is rarely required; however macros may need a
certain data block type. Changing the data block type only renames the data
block. The data is not affected.
Copy the data block to be changed into the box and select the desired type from
the list. Not all data block types may be available.

File
Figure 37: Change Data Block Type
3.19 New and Open
By selecting New you open a dialog from which you can choose OPUS, PLE or
VB Script. OPUS generates a new OPUS workspace (see chapter 14.10), PLE a
blank template for the Plot Layout Editor (see chapter 11.5) and VB Script a
blank VisualBasic script form. You find detailed information about writing VB
Scripts in the “OPUS Programming” manual.
Open opens an existing OPUS workspace.
3.20 Printing
You can print a report on your default printer using the Print command. Printing
spectra and creating templates for printing will be discussed in section 11.
3.21 Print Preview
This command is only available for printing reports; it will give you a preview
of the printout.
3.22 Print Setup
A default printer can be defined using your Printer dialog box. You can specify
the paper size and orientation, they will be kept as default for further OPUS
printouts.

Edit Parameter
4 Edit
The Edit menu lists all features for the information input and functions dealing
with structure editing as well as the standard Windows functions like Copy and
Paste.
Figure 38: Edit Menu
4.1 Edit Parameter
Crucial sample parameters like sample name, sample form, operator name and
sample number can be edited with the Edit Parameter command. Select the
spectrum on the first tab of the Edit Parameter dialog. Note that in GLP mode,
you can not edit this parameters.

Edit
Figure 39: Edit Parameter – Enter Parameter
On the second tab you can set the axes labels and a scaling factor to be used
when displaying the spectra.
Figure 40: Edit Parameter – Axes Labels

Replay
4.2 Replay
When you are working in a GLP environment a copy of the original spectrum,
i.e. a spectrum before any manipulation is carried out, is saved with your data.
Based on this original spectrum, you are able to “Replay” parts of the manipula-
tion carried out so far.
Figure 41: History Replay Function
Load the spectrum to replay into the window “File for Replay” by dragging the
file icon into the box. Now select in the manipulation up to where you want to
restore the file. If you choose Smooth in the example in Figure 41, Baseline,
Normalize and Smooth will be carried out on the original spectrum, but not
Peak Pick.
4.3 Information Input
Besides the OPUS parameters you can save additional information describing
your samples using the Information Input function. Your input will be saved in
an additional information block . You can include this information in a
report window as well as in a plot. The creation of an information block is man-
datory if you want to add your sample to a library file.
In order to attach information to your data files you first need to create an infor-
mation mask (refer to chapter 4.4). To use an existing information mask for data
input, load a spectrum into the Browser and select it. From the Edit menu

Edit
choose Information Input; the most recently used information mask will be dis-
played.
Figure 42: Information Mask
You can only choose one spectrum file at a time to enter additional information.
The name of the information mask used for data input is indicated in the Text
Definition field. To use another information mask click on New Text Mask; a
dialog box will appear from which you can select a different information mask.
Enter the information you want to attach to your sample file. You do not need to
fill out every field. After you are done save your input using the Add Informa-
tion button. A new data block will be attached to your spectrum file. Now right-
click on the data block icon in the Browser and select Show Report; this will
open a report window which displays the information you just entered.
4.3.1 Editing Existing Information Blocks

You can use the Information Input command to edit existing information
blocks. If an OPUS file already has an information block attached it will auto-
matically be opened by the Information Input command using the correct infor-
mation mask. However, if the appropriate mask cannot be found the name of the
mask will be highlighted in red.

Creating an Information Mask
Now you can alter or add the information block. Alternatively, you can select a
different information mask; in this case all existing information will be dis-
carded. If you accidentally modified or deleted fields you can restore the origi-
nal data set using the Restore Information command.
4.3.2 Creating a New File

Instead of attaching an information block to an existing OPUS file you can also
create a new file, which then only consists of an information block. In this case
check the New File box. A new file called INFOx.0 will be created, x being a
the number of the file.
4.3.3 Displaying and Printing Information Blocks

As already mentioned the information block can be displayed in a report win-
dow. To print an information block you can treat each line of the block as an
OPUS parameter. Each line can be addressed using the parameter name Inn, nn
being the line number (e.g. I12 stands for the twelfth line). In the same way you
can include the names of the fields in the information mask into the plot, using
Tnn as parameter name.
4.4 Creating an Information Mask
OPUS allows you to create and modify information masks which you can use
for data input. An information mask can consist of up to 99 fields.
By creating an information mask you define the kind of information you will
save in conjunction with your sample. You can create various information
masks to cover all types of samples. The content and the name of the informa-
tion mask will be saved together with the information you enter. This allows a
convenient transfer of all the information together with your data files to
another computer. You can always call up the information you entered even if
you created the information mask on a different computer.
To create an information mask load your spectrum as usual and select it in the
Browser. If you have already created information masks the content of the mask
most recently used will be displayed. Choose Setup Info Mask. You will see the
following dialog box:

Edit
Figure 43: Setup Info Mask
If no masks exist the dialog box will be empty. You can clear the dialog box
using the Clear All button. Now create a new mask by successively entering the
names of the fields you want displayed in the mask. Blank lines are not allowed.

Structure Import
Figure 44: Defining Information Mask Fields
After line 11 you can add another tab using the Next Page button. If you have
finished, save your definition by clicking on Save Definition. If a mask with the
same name already exists, you will be warned and asked whether you wish to
overwrite the existing mask.
To edit an existing mask load it into the Setup Info Mask dialog box and modify
it. You can discard the changes you have made by clicking Restore Original.
4.5 Structure Import
You can import and convert chemical structures available in Molfile format
developed by MDL and widely used by third party software. The Structure
Import command opens a standard Load File dialog box, which allows to load
files with the extension .mol. Select one or more files to be converted. For each
file, an OPUS file with the same name and a consecutively numbered extension,
starting with 0, will be created and automatically loaded into the OPUS
Browser. To view a structure, double-click on the structure data block; this will
open a structure view window. To attach a structure to an OPUS file see 4.7.

Edit
4.6 Edit/Create Structure
This dialog presents a general interface to any commercially available third

party structure design software that reads and writes Molfile format. You can
use an editor of your choice. Bruker also offers a third-party structure editor
suited for this interface.
An OPUS file will be automatically converted to Molfile format and stored in

the search subdirectory as BISRY.MOL. The path and file name of this file is
forwarded to the structure editor via the command line. If your editor is capable
of handling command line parameters the structure will then be automatically
displayed. Depending on your editor, you either can exit the editor and confirm
to store the changes, or you need to explicitly store the changes in Molfile for-
mat first after modifying the structure. The altered file will then be automati-
cally converted back to OPUS format.
If you select New Structure File OPUS creates an empty file and passes it on to
the editor.
Figure 45: Edit/Create Structure – Edit Structure
On the first tab you specify whether you want to create a new structure file (in
this case select the New Structure File checkbox) or to edit an existing structure.
To do this drag the file containing the structure onto the window and click on
the Edit/Create Structure button. If you create a new structure file you have to
specify the file name and path (or use the Browse button) of this file.

Attach Structure
Figure 46: Edit/Create Structure – Choose Editor
You can specify which editor you would like to use in combination with the
Edit/Create Structure command. Type the name of the program, including the
path statement, into the Structure Editor line or browse the directories with the
help of the Browse button. The Scaling Factor determines the size of an
imported structure.
4.7 Attach Structure
After you imported a chemical structure you can attach this file to an OPUS
spectrum file. The file will be automatically converted into OPUS format. Load
the spectrum in the OPUS Browser and drag it on the Select OPUS Spectrum
box. Enter the name of the structure file to be attached, including the path.
Alternatively, use the Browse button to locate the file. Click on Attach Structure
to include the structure in the OPUS file.

Edit
Figure 47: Attach Structure

Toolbars
5 View
The View menu allows to configure the OPUS user interface. You can define
the toolbars, hide or unhide the status bar or the browser window.
Figure 48: View Menu
5.1 Toolbars
Use the Toolbars option from the View menu or right click onto the OPUS tool-
bar to open the Toolbars dialog. This dialog allows to configure single tools or
even complete toolbars.
Figure 49: Toolbars Configuration
If you check the boxes listed, you can activate or deactivate the different tool-
bars. Click on the New button to create new toolbars. Customize allows you to
adjust the toolbar according to your individual preferences. A second dialog box
will open.

View
Figure 50: Customize Dialog Box
Use the Toolbars tab to select the toolbar you want to customize. If you check
Show Tooltips, additional info text pops up which describes the function of a
specific icon when you position the cursor on it. New Look means that the line
between the icons on the toolbar will not be displayed. This is set by default. To
enlarge the icons displayed, check Large Buttons.
The Commands tab allows to select different categories and have the exact
description of each button displayed. You can drag the icons directly into the
toolbar. If you want to remove an icon from the toolbar, simply drag the specific
icon from the toolbar and drop it outside the bar.

Status Bar
Figure 51: Customize – Commands
5.2 Status Bar
The status bar informs about background tasks of programs running in the
OPUS environment, and indicates their current status. To activate or deactivate
the status bar, check the Status Bar option.
5.3 Browser
By default, the OPUS user interface always displays the browser window on the
left side. If you deactivate the Browser option, only the spectrum and overview
window will be displayed on the screen. Besides these options you can also
reposition the OPUS browser window (see section 6.4)

View

New Spectrum Window
6 Window
The Window menu allows you to customize the position and appearance of the
spectrum and report windows.
Figure 52: Window Menu
6.1 New Spectrum Window
When using OPUS it is possible to display several spectra in the one spectrum
window, and to display spectra in different windows. If you select the New
Spectrum Window option a new spectrum window opens, indicated by the
tab at the bottom of the spectrum window. Click on the respec-
tive tab to be able to switch between the windows.
6.2 New Report Window
OPUS uses report windows to display data other than spectra or interferograms.
For example, the results of a peak picking evaluation and its parameters
used can be listed numerically. The data are displayed by dragging the peak
pick data block into the report window.
6.3 New Registered Window
If you click on the New Registered Window option, a drop-down list opens
which includes all possible types of OPUS windows. The number of windows
may vary, according to the additional software packages installed. Therefore,
the list in this manual may not exactly reflect the list contents displayed on your
screen. You can open any type of blank window by selecting the window from
this list.

Window
Window Name Type

3d, 3d+ Window used to display three-dimensional plots.
Cluster Analysis Part of the OPUS IDENT package, window used to display a
dendrogram or histogram.
Display Window used to display spectra.
Library Window used to display libraries and their detailed informa-
tion.
OldReport Shows report in the OPUS/OS2 format.
Process Control Part of the PROCESS package, window used to display a
standard trend chart.
Report Window used to display report blocks.
SearchResults Window used to display the result of a search performed
using Spectrum Search and other Search functions.
SingleReport Displays report without the tree structure.
Structure Part of the SEARCH package, window used to display
molecular structures, generated with a structure editor.
Text View Window used to enter text. See section 6.3.1.
6.3.1 Text View

Select Text View from the drop-down list. The Text View window opens. There
are three possibilities to enter text into the OPUS Text View window:
1) Keyboard
Place the cursor into the window and enter text using your keyboard.
2) Copy and Paste
It is possible to copy and paste text in the Text View using the shortcut
Ctrl+C and Ctrl+V.
3) Drag and Drop a text file
Drag and drop a text file in the Text View window.
You can only drag one file into the Text View window. If there has been
already a text file in the Text View window, this file will be replaced and
the text is overwritten unless you press the STRG key during the Drag
and Drop operation. In this case the text of the dragged file is appended
to the content of the file which has already been open.
To select text within the Text View window, click on the left mouse button, hold
it down and move the cursor to the relevant text passage. You can also use the
Shift and one arrow key. If you want to delete text, you can either use the Back-
space ( ← ) or Delete key, or you select the text and use the STRG+X shortcut. It
is also possible to use the Cut command from the Edit menu.
To save a text file, right click on the Text View window and select the Save
option from the pop-up menu.

Cascade and Tile Windows
6.4 Cascade and Tile Windows
You can either cascade or tile the different windows, see Figure 53 and 54.
Figure 53: OPUS User Interface – Tiled Windows

Window
Figure 54: OPUS User Interface – Cascaded Windows

Arrange Icons
In connection with the OPUS browser pop-up menu you can further configure
the appearance of your OPUS interface. Right click onto the browser window
and the following menu pops up:
Figure 55: Browser Pop-Up Menu
If you select Allow Docking, the windows (browser, spectrum and overview
window) are displayed next to each other within the OPUS interface. If you
deactivated this option, you can remove the browser window from the OPUS
interface and position it somewhere on the Windows desktop.
The Hide option makes the browser window invisible. To restore this setting,
activate Browser in the View menu.
Float In Main Window opens the browser and spectrum window in equal size
on the OPUS user interface. You can switch between these two windows by
using the relevant tabs at the bottom.
6.5 Arrange Icons
If you have minimized several spectrum or report windows, you can have their
icons arranged according to the Windows settings. By default, the icons are
arranged at the bottom of the OPUS user interface.

Window

Configuration of the Optics
7 Measure
All functions applicable to the instrument setup and data acquits it ion are found
in the Measure menu. OPUS allows you not only to configure and adjust your
spectrometer but also to define different sets of experiments which you can save
and reload for future use. Furthermore you can use OPUS to control additional
equipment as well as have your data acquisition triggered by external sources.
In case the communication with the spectrometer is established through an Eth-
ernet port ensure you have Microsoft Internet Explorer 5.0 or higher installed.
Figure 56: Measure Menu
A BRUKER service technician has configured your copy of OPUS to match

your spectrometer optics when your spectrometer was installed. If you change
or modify parts of the optics you must adjust the settings of OPUS.
7.1 Configuration of the Optics
BRUKER spectrometers can be configured to best fit your experimental tasks.

The definitions and parameters of your optics are accessible by the Optic Setup
and Service command. On the first tab of the Setup Dialog the spectrometer
model can be chosen and the general status of the acquisition processor (AQP)
is displayed.

Measure
Figure 57: Optics Setup – Select Spectrometer Model (AQP)
Optical bench type lists your spectrometer model; if the spectrometer is work-
ing correctly you will find the characteristics of your spectrometer indicated
(Optical Bench Type, AQP Driver, AQP Memory Size and AQP Software).
AQP simulates an Optic Bench disables communication between OPUS and

your spectrometer. If you want spectrometer control make sure this is not
checked. If this option is checked, all measurement commands are executed in
simulation mode and not on the optic bench. The AQP generates synthetic inter-
ferograms with some artificial noise. Use this mode to check if problems are
caused by the optics or by the AQP.
For spectrometers with ethernet connection like the MATRIX or TENSOR

series, no AQP is installed. These instruments are connected via network and
have a URL (Uniform Resource Locator) that needs to be specified in the setup.
Therefore the Optical Bench tab looks slightly different:

Figure 58: Optics Setup – Select Spectrometer Model (Network)
All other parameters concerning the optics are listed on the next tab, Devices/
Option. This tab serves to specify the components installed in your spectrome-
ter. To activate a component, select the respective check box.

Measure
Figure 59: Optics Setup – Device Configuration
All available options can be configured using the Setup buttons. As an example,
the configuration of the detector is shown:
Figure 60: Detector Configuration Menu

A test ramp is available for testing and diagnostics of the detector port. Two
detectors are present, a DTGS detector and an additional MCT detector. An
additional entry allows for the addition of new hardware to your spectrometer,
i.e. here the MCT detector. To do this, press Add New Item and enter 2 = MCT
in the command line. This entry will be displayed in black in the device table,
symbolizing an editable entry. If a device is momentarily not available simply
remove the mark in its check box. You can change the hierarchy of the device
table entries by moving lines up or down using the respective buttons. Confirm
your changes with OK or discard them clicking on Cancel.
Some detectors such as MCT detectors generate a non-linear response with

respect to concentration and intensity. In order to user these detectors when per-
forming quantitative analysis it is necessary to correct for the non-linear
response. A non-linear response will result in non-zero intensities appearing in
the spectral regions where zero intensity is expected. By determining the value
of the intensity in the expected zero region, and comparing this to the total
intensity reaching the detector, the degree of the detector non-linearity can be
computed. This factor can then be applied to the measured data to correct for the
non-linear response.
To perform this non-linearity correction routinely, some additional parameters

have to be defined for the particular detector. In order to determine the value of
these parameters it will be necessary to first collect a single channel measure-
ment using the particular detector. When performing this measurement it is
important that you do not use any type of filtering (optical or electronic). The
parameters which have to be defined for the detector entered in the following
way:
Detector; low wave number cutoff frequency; modulation efficiency
(i.e. MCT;450;1.0, see Figure 60)
For a successful non-linearity correction the following conditions must be

matched:
1) The spectrum must be collected from zero wave numbers up to the max-
imum wave number at which the detector produces a signal.
2) Electronic filtering is not allowed. The measurement bandwidth must be
sufficiently broad to prevent folding effects.
3) The FT parameter Phase Resolution must be set such that the value of
Phase Interferogram Points is not less than 500 points. Choice of too
low a phase resolution causes an inaccurate non-linearity correction.
You can influence the content of OPUS files using the Setup Result Spectrum
command. The direct result of a data acquisition is always an interferogram.
The interferogram can be transformed into spectra of various types, for example
absorbance, transmittance or reflectance spectra. A result type will only be
available when setting up an experiment if you enable the result type in the
Setup Result Spectrum list.

Measure
Figure 61: Setup Result Spectrum
Considerations for Raman Experiments

If a laser is used as a light source you have to specify its wavelength and maxi-
mum power output. A special format is used for these entries, which is
explained on the bottom of the laser setup dialog.
Figure 62: Source Settings

On the third tab of the Optic Setup&Service dialog you can set the values for the
absolute peak position, the laser wave number, the resolution, data rate and the
maximum FT size. You need to evaluate the absolute peak position of your sys-
tem using the Check Signal command (see „Check Signal” on page 75). This
parameter has to be determined every time the optics have been adjusted or if
the laser or the detector is changed. For multi-channel operation, the laser wave
number can be specified individually for each channel if a channel-specific IT-
Test is available.
Figure 63: Interferometer/AQP Settings
You can specify the file format of an OPUS data file on the Export Options tab.
The default is to save a file in OPUS format. However, you can also export the
data to GRAMS format. Keep in mind that the GRAMS software has to be run-
ning on your computer while you export the data.

Measure
Figure 64: Export Options – Defining the File Format
On the Service tab you find the OPUS diagnostic functions. The display win-
dow lists the test results and statistics of your spectrometer. However, the optics
test must have been performed at least once after the installation of OPUS, oth-
erwise no test results are available. You can repeat the test by clicking on
Repeat Diagnostics Test. The buttons on the right side of the box reset the
instrument parameters.
The topmost buttons concern the parameters of the HeNe laser; some lasers
show sporadic power fluctuations during operation, which disturb the spectrom-
eter control. These fluctuations are recorded automatically by an internal
counter. The count should always be zero, in case of an increase of these fluctu-
ations the laser should be replaced.
Reset Laser Dropouts resets this counter (e.g. after a laser replacement). Laser
Replaced resets the counter of the total operation time of the laser and in addi-
tion reads the value of the laser intensity.
Source Replaced performs the similar operation on the counter of the total
source operation time and the counter of the on/off cycles of the source.
The rest of the buttons affect the spectrometers’ stepper motors; the number and
position of stepper motors depends on the spectrometer type. Update whole
Motor Table reads the parameters of all motors present in your spectrometer.
The other buttons read the status of specific motors:

• Update Aperture Motor Table – motors that control the aperture

• Update Channel Motor Table – motor to switch beam ports
• Update Detector Motor Table – motor to switch detectors
• Update Source Motor Table – motor to switch sources
• Update Calibration Filter Motor Table – motor that controls the cali-
bration filter
• Update Polarizer Motor Table – motor which controls the polarizer
• Update Sample Changer Motor Table – motor which moves the sam-
ple wheel
• Update Flaps Motor Table – motors that controls the flaps
Figure 65: Service
The Optic Setup dialog serves to monitor the AQP communication. Check the
Autoscroll box if you want the list to scroll while displaying the output.

Measure
Figure 66: Optic Communication
7.2 Measurement
After you have configured your spectrometer you can start to set up an experi-
ment. There are basically two types of measurement modes possible: the
Advanced Measurement and the Routine Measurement. The difference between
those two modes is the number of parameters you can set up. In the Advanced
Measurement mode you have access to all parameters, whereas in the Routine
Measurement mode, a preselection of parameters best suiting your instrument,
has been carried out and you only need to select very few parameters to perform
a measurement. Please note that Routine Measurement is not available for all
instruments.
When you are working in a validated environment (see Chapter 14.10), the
Setup Measurement Parameters function allows you to load and edit a measure-
ment without giving you the option to perform this measurement.
Special considerations and conditions necessary for Raman measurements can

be found in the last section.
When OPUS is started, the last parameter set used in the previous OPUS session
will be loaded by default. If this is the experiment you wish to use you can con-
tinue, otherwise you will have to load a new experiment.

Measurement
By clicking on Exit you will save all parameter fields in the Measurement dia-
log box, except the peak position of the interferogram. This has to be saved
explicitly using the Save Peak Position button. Cancel exits the dialog box
without saving any of the changes made. You can use this function as an undo
command (for all changes made except saved peak positions). Also you can
save a parameter set as an experiment file (see page 68).
7.2.1 Basic Parameters

The basic parameters for the data acquisition are found on the first tab of the
Measurement Dialog box.
Figure 67: Measurement – Basic Parameters
From this tab you can either load an existing experiment file or create a new
experiment (see below), specify your sample, and check the path and name for
the experiment file. This information is optional and will be stored in the data
file. When the measurement parameters differ from the parameters in the loaded
experiment, the name of the experiment is highlighted in yellow. In addition,
these parameters are listed in the history block of the recorded spectra.
If you loaded an existing parameter set or would like to acquire a spectrum

using the default settings, you can start an acquisition with Background Single
Channel and Sample Single Channel. When the acquisition has finished the
spectrum will be automatically saved to disk. The parameters used for the
acquisition are stored together with the experimental data. These parameters are
accessible via the OPUS Browser pop-up menu (see chapter 2.2).

Measure
While an acquisition is running, the progress of the measurement is indicated by

a status bar in the lower right edge of the OPUS window. Right-clicking on the
status bar opens a pop-up menu, which allows you to abort the measurement.
Stop Task interrupts an ongoing measurement (a repeated measurement will
continue with the next spectrum) and Abort Task interrupts a repeated measure-
ment. After the completion of the data collection “No Active Task” is displayed
in the status bar.
Except for Emission, Raman or Single Channel spectra it is always necessary to

acquire a background spectrum, to eliminate the frequency characteristics of the
source, the spectrometer and absorption of the sample matrix. This correction is
done automatically after the sample measurement is completed. The sample
spectrum then is divided by the background spectrum to generate an absorbance
or transmittance spectrum.
7.2.2 Advanced Settings

The Advanced Settings dialog offers you the possibility to fine tune your exper-
iment. Furthermore, you can change the data file name and the path where the
file will be saved. The default path is the Meas subdirectory of your OPUS
directory, the default file name is Work.xxx.
Figure 68: Measurement – Advanced Settings
Enter the acquisition parameters (resolution, scan time, number of scans and
scan range) and define the data type to be saved. The resolution should not be

Measurement
set any higher than necessary to minimize the acquisition time. Doubling the
resolution requires a four times higher acquisition time to achieve the same Sig-
nal-to-Noise ratio. The Signal-to-Noise ratio of a spectrum is proportional to the
square root of the acquisition time. Hence, an improvement of the Signal-to-
Noise ratio by a factor of 2 requires an acquisition time that is four times longer
than the time initially chosen for the measurement.
You can also pre-select the type of the result spectrum (here transmittance). If
you choose to save the interferograms you are able to calculate all result spectra
afterwards. Remember that only the result spectrum types that you have enabled
in the Optic Setup will be displayed here. You can use the Save button to save
these settings in an experiment file.
7.2.3 Optics Parameter

The Optics Parameter tab define the type of source and detector you use, the
aperture size, the channel and the scanner velocity. Also, the settings for the
preamplifier can be changed here.
Figure 69: Measurement – Optics
Choose an aperture setting from the aperture pull-down list. The size of the
aperture defines the spectral resolution. Using an aperture diameter, A, you
achieve a peak broadening1 δσ (at a fixed focal length F ) at a wave number σ
of:
1.More accurate: a convolution with a delta function of width δσ.

Measure
A2
δσ ≥ --------2- ⋅ σ
8F
Select the channel you want to use for the measurement (e.g. Front, Back or
External), and specify a detector if your spectrometer is equipped with several
detectors. In addition you can choose between four preamplifier settings (only
important for the IFS 120HR).
The best scanner velocity depends on the type of detector and the actual experi-
ment. Choose slow scanner velocities (< 10kHz) for photoaccoustic experi-
ments. 10kHz is adequate for DTGS detectors and photodiodes, while you
should use higher velocities (> 10kHz) if you use MCT or InSb detectors.
We recommend to set the Sample Signal Gain and Background Signal Gain val-
ues to “Automatic”. The best value is then determined during one scan before
the measurement starts, to ensure that the complete dynamic range of the ADC
will be used.
The Switch Gain setting allows you to amplify the interferogram by 2N in a

region further away from the centerburst; this corresponds to an enhancement of
the ADC dynamic from e.g. 16 to (16 + N) bit and reduces the digital noise.
This is important for data acquisition in high resolution while using a broad
band source. The distance from the center burst can be specified in the Window
in Points field.
You can program the spectrometer to pause using Delay after Device Change
after a change (like an automatic sample change or a detector change) was per-
formed. Set a delay time before the measurement start by entering the time in
sec. in the Delay Before Measurement window. The delay is an option to pre-
vent detector overload (especially for slow detectors) if certain parameters such
as sample changer position, detector, measurement channel etc. have been
changed.
7.2.4 Acquisition Parameters

Set the desired frequency range for the Fourier transformation in the topmost
two fields of the acquisition dialog. The actual calculated limits may deviate
from these values and are therefore indicated on the right hand side.
Restricting the sampling bandwidth reduces the amount of data and may be ade-
quate when recording high resolution spectra. However, electronic and digital
filters have to be used to cut the signal intensity to zero beyond the chosen fre-
quency limits. Otherwise, intensities existent outside the measured frequency
range can potentially be convoluted (or “folded”) into the measured frequency
range.

Measurement
Figure 70: Measurement – Acquisition
In addition, the low pass filter, the high pass filter, the acquisition mode (defin-
ing whether one or both sides of the interferogram will be measured) and the
correlation mode (which is a data integrity check) can be set here.
Since the interferometer mirror is continuously moving, all frequency compo-

nents of the IR spectrum are depicted in a “detector response spectrum”. This
lies in a lower frequency range and its bandwidth can be limited by using elec-
tronic filters.
The high pass filter limits the bandwidth in the high frequency region. Set it to
“ON” to activate the filter and to “OPEN” to deactivate it. Note that this elec-
tronic filter is not available for all spectrometers.
Use the low pass filter to limit the bandwidth in the low frequency region. In the
low frequency region, the mapping of the IR wave numbers to frequencies is
proportional to the scanner velocity v; a fixed frequency limit f of the filter (in
Hz) corresponds to a wave number σ which depends on the frequency v accord-
ing to:
σ [ cm –1 ] = f [ Hz ] ⁄ v [ cms – 1 ]

Measure
For the acquisition mode there are the following options:
• Single Sided: this option allows only one-sided interferograms to be

measured, data is acquired during the forward movement of the mir-
ror.
• Double Sided: the interferogram is measured on both sides, data is
acquired during the forward movement of the mirror. This mode
yields an improvement of 2 in the signal-to-noise ratio as com-
pared to the Single Sided mode. The resolution in time however
amounts to half the value achieved in Single Sided mode. Double
Sided acquisition is the method of choice for Raman, Emission,
Phase correction mode Power, and precise quantitative measure-
ments.
• Forward/Backward: data is collected during the forward and back-
ward scan of the mirror. Forward and backward scans are co-added
separately, calculated and then added. This mode has less dead time
and a better signal-to-noise ratio, but requires twice as much compu-
tation time.
• Fast Return: this mode offers a fast mirror retrace without data col-
lection; there is less dead time and a better signal-to-noise ratio.
Fast Return and Forward/Backward modes are not available for all types of
spectrometers. For the same acquisition time the signal-to-noise ratio improves
in the following order:
S/N (no Fast Return) < S/N (Fast Return) < S/N (Forward/Backward)
The Correlation Mode determines whether a data integrity check is performed

during the acquisition:
• No: the data will not be checked.

• Around Peak, low: is only available, if multiple scans are averaged.
Every new interferogram is compared to the first one in a range
around the centerburst. If the deviation exceeds the threshold the
scan will be discarded.
• Around Peak, high: same as low, but sensitive to smaller changes
(like thermal fluctuations).
• Full Igram length: In contrast to the above modes, all points of the
new interferogram are compared. In case of deviations, the area that
diverges is replaced by the corresponding part of the average spec-
trum. Scans are discarded only if they contain more than ten defec-
tive areas or if the number of defective points exceeds one eighth of
the total number of interferogram points.
This method was especially developed to correct the myon-spikes
from Raman detectors. Due to its higher computation time it can only
be used for slower mirror velocities.

Measurement
7.2.5 Fourier Transformation Parameters

Set the phase resolution to a value which gives at least 250 phase interferogram
points (shown on the right hand side). Choose an appropriate phase correction
mode to symmetrize the interferogram. The Phase Resolution value cannot be
smaller than the measurement resolution and cannot exceed 8192 points.
The phase correction symmetrizes the interferogram. Phase correction is always

necessary since the measured interferogram is never perfectly symmetric. See
chapter 8.15 for a description of the methods.
The value of the zerofilling factor has to be of the order of 2n, zerofilling adds
data points to the interferogram and therefore results in better line shapes.
Figure 71: Measurement – Fourier Transformation
7.2.6 Display
The axes settings of the displayed spectrum during measurement can be
changed here. You can define upper and lower limits for the x- and y-axis. Dis-
play single scans before measurement performs scans before starting the data
acquisition and calculates the spectrum. The actual recording is started when the
operator starts the measurement.

Measure
Figure 72: Measurement – Display
7.2.7 Background
The background spectrum stays resident in the AQP and will not be saved auto-
matically. If you would like to save it to your hard disk you have to do so
explicitly with Save Background. You can also clear the AQP memory by click-
ing on Clear Background or load an older background spectrum using Load
Background. Alternatively, drag the background spectrum from the Browser to
the command line of the dialog box. For MATRIX and TENSOR spectrome-
ters, the background is saved in a file called “OPUS.BG” in the OPUS direc-
tory. Upon starting the OPUS software the background spectrum used last will
be loaded automatically.

Measurement
Figure 73: Measurement – Background
7.2.8 Check Signal

The appearance of this tab depends on the configuration of your spectrometer.
Besides the options and commands shown here you may find additional func-
tions on this tab for your system.
You need to call up this tab at least once, after your spectrometer was installed,
to determine and save the exact position of the interferogram. This tab is
intended to both optimize the shape of the single channel spectrum and to
achieve a maximum count rate of the interferogram.

Measure
Figure 74: Check Signal Box with Interferogram
Similar to the spectrum display you can zoom into the displayed region. All Fig-
ures shown here may differ from the interferogram obtained on your system.
Figure 75: Enlarged Interferogram
You can switch back to the original size of the displayed region (Scale Display)
and shift along the x-axis using the and buttons in the case that no
interferogram can be observed. The amplitude maximum and the position of

Measurement
this maximum can be read at the upper window bar. When you read constant
values here, save the peak position using the Save Peak Position button.
The numerical display tool allows you to monitor the interferogram position
from a distance to help you to adjust the interferometer. You switch to the
numerical display by clicking the ADC Count radio button.
Figure 76: Numerical Display Tool
Choose Interferogram to return to the graphical display or Spectrum to Fourier

transform the interferogram to obtain a single channel spectrum.
Stepper Motor Adjustment

If your spectrometer has the option of software controlled adjustment of the
interferometer using stepper motors, the motor control panel is displayed in the
upper part of the control field. The motor positions should be varied until the
absolute maximum in count rate (largest amplitude) is found.
Figure 77: Stepper Motor Control
The motors can be moved using either the manual control or Auto Align. Auto
Align performs an auto-adjustment to locate the maximum of the interferogram.
Use the Fine Auto Align command to correct minor misalignment of the motors.
This command covers a smaller range of motor movement and therefore works
faster than Auto Align. This is especially recommended if you measure spectral
regions of higher frequency (NIR to UV).
By clicking on Exit you will save all settings made in the Measurement dialog
box so far, except the peak position of the interferogram. This has to be saved
explicitly using the Save Peak Position button.

Measure
7.2.9 Error and Warning Symbols

In case of a mismatch between the software configuration and your hardware
several symbols indicate the source of error. A warning sign indicates either:
a) A loaded method is not compatible with the hardware configuration.
b) The value of a parameter is not within its limits.
Example 1:
Figure 78: Error – Wrong Source
Next to the tab Optic a red “Error” symbol indicates a parameter mismatch with
the existing hardware. The dialog field Source is marked red to indicate that
“Globar” was entered as radiation source, but a globar source is not present in
the instrument. If you point the cursor to the field a help text is displayed, refer-
ring to the source of error.
Example 2:
Figure 79: Warning – Resolution too Small
If the value of a parameter is not within the allowed limits a “Caution” sign will
appear. Again a help text refers to the source of error; in this case the resolution
was set to a too small value.
Example 3:
However, a warning sign will not necessarily be displayed at the location of the
mistake. If you set a wrong value for the frequency range a warning will appear
on the Advanced tab.

Measurement
Changed from
to
Figure 80: Warning Resulting from Frequency Change
Example 4:
In this example the resolution was set to 1 cm-1 and the frequency range from
4000 cm-1 to 400 cm-1. 10 mm was chosen as aperture size. As a result an infor-
mation sign indicates that the acquisition is possible, however due to the param-
eter set the resolution will be limited above 1300 cm-1.
Figure 81: Information Sign
Example 5:
Using user profiles it is possible to prohibit any changes of the parameter sets.
In the worst case a parameter was set wrong but cannot be corrected because the
user who logged into OPUS does not have the privileges to do so. This will be
indicated by an “X”.
Figure 82: User has Insufficient Privileges
In this case the user has only the choice to use another experiment file or to call
the OPUS administrator to correct the error.

Measure
7.2.10 Raman Experiments

On the Basic tab (see page 67) the laser power can be specified. The laser will
be shut down after each acquisition by default. If this is not desired you can turn
this option off by deactivating the checkbox.
Figure 83: Raman Measurement – Showing Auto Laser OFF Checkbox
On the Advanced tab the frequency range will be shown with respect to the laser
excitation frequency. This will be indicated by a yellow background. Also, the
acquisition parameters will be given in relation to the laser excitation frequency.

Measurement
Figure 84: Raman Measurement – Frequency Range Referred to Laser Line
All frequencies of the acquisition parameters will also be shown and refer to the
laser excitation energy.

Measure
Figure 85: Raman Measurement – Frequencies Limits Referred to Laser Line
The laser power can be set using a switch on the Check Signal tab.

Repeated Measurements
Figure 86: Check Signal Tab – Laser Power Slide Control
7.3 Repeated Measurements
The Repeated Measurements command allows you to define a measurement

series to automate data acquisition. The Repeated Measurements dialog differs
from the Measurements dialog only in the first tab; in addition, you can enter
the number of total scans and the delay between measurements here.

Measure
Figure 87: Repeated Measurements – Basic Settings
7.4 Rapid Scan -

Time-Resolved Measurements
Rapid Scan time-resolved measurements allow you to acquire spectra in quick

succession. Typically, time-resolved measurements are performed to study
dynamic phenomena of the sample or environmental fluctuations. Also, the
time intervals between data acquisition can be repeated with high precision. The
results of a Step Scan experiment are stored in a 3D file, which holds all spectra.
Contrary to the OPUS/CHROM software, no spectrum or chromatogram will be

calculated during the acquisition. Therefore, TRS measurements require no
additional computational power or any additional CPU capacity on your AQP
board. However, the AQP has to have sufficient RAM to store all averaged
interferograms. The following table lists the maximum number of interfero-
grams per run, using a bandwidth of 0 – 7900cm-1 and single sided acquisition.
AQP Memory Max. Number of Interfero- Max. Number of Interfero-

grams (8 cm-1) grams (4 cm-1)
1 MB 67 33

Rapid Scan - Time-Resolved Measurements
AQP Memory Max. Number of Interfero- Max. Number of Interfero-

grams (8 cm-1) grams (4 cm-1)
4 MB 480 240
16 MB 2130 1065
Figure 88: Rapid Scan Time Resolved Measurements – Method Editor
Basically, the Rapid Scan Time Resolved Measurement dialog box is identical
to the Measurement dialog (described in chapter 7.2), except for the Method
Editor tab. Here you define the timer parameters of your experiment. The but-
ton New opens a blank method page.
The following functions are used to construct a measurement sequence:
• Measurement of single scans

• Measurement of several average scans
• Waiting for an external TTL-signal
• Output of an TTL-signal
• Output of optic commands
• Message to the operator, wait for operator response
• Wait times
• Start loop/end loop (repetition of a sequence)

Measure
Use the buttons on the right side of the Method Editor to program these com-
mands. However, you can also manually enter and edit the program code in the
window.
• Message Box: This button inserts the command “Message box xxxx”;
where xxxx is a spacer for the text that will be displayed when run-
ning the TRS method. Change the spacer to the text you want to print
on the screen.
• Comment: Comments can be used to make the program code easier to
read.
• Optic Command: This enables the user to send text commands to the
optics at run time. This is useful to change certain parameters during
the execution of the experiment.
• Set Buffer: Set Buffer specifies the part of the memory which will be
accessed. You can use the same memory section repeatedly.
Example:
Measure 10 Scans to Buffer 5
Writes 10 scans to buffer 5

Buffer=1
Start Loop=100
Measure 1 Scan
End Loop
Writes 10 scans to the buffers 1 to 100
• Start Loop: In combination with End Loop, these commands can be

used to achieve an n-fold repetition of all command enclosed
between these statements. You can nest these loops as often as you
want as long as for every Start Loop statement there also exists an
End Loop statement.
• End Loop: Marks the end of a loop.
• Wait (ms): The execution of the following command will be delayed
by the amount of milliseconds specified here.
• Reset Time Base: The time information stored with the spectra is
measured relative to the start time of the measurement. If a Reset
Time Base command is executed the time base is reset to zero.
• Wait Input “High”: This feature delays the following command until
the TTL level 5V is detected. The table below explains the correla-
tion between the bits and the pins of the 50-pole I/O plug. The bit
marked with an (s) is read using an especially fast command and
should be used when very fast time resolution is required.
Bit Number Pin Number Socket Pin Number Plug
4 13 5

Rapid Scan - Time-Resolved Measurements
5 14 38
6 15 22
7 (s) 16 6
• Wait Input “Low”: This feature delays the following command until
the TTL level 0V is detected.
• Set Output “High”: This command sets a TTL level of 5V to the
specified output pin. The table below explains the correlation
between the bits and the pins of the 50-pole I/O plug. The bit marked
with an (s) is read using an especially fast command and should be
used when very fast time resolution is required.
0 5 35
1 6 19
2 7 3
3 (s) 8 36
• Set Output “Low”: This command sets a TTL level of 0V to the

specified output pin.
• Measure NSS Scans: The total number of scans to average will be
read from the Measurement dialog. This has the advantage that it is
not necessary to write a new TRS method, in case this method should
run with different numbers of scans.
• Measure N Scans: This command starts the data acquisition. The
total number of scans has to be stated after the Measure command.
Figure 88 shows the program code generated by these buttons. There are three
checkboxes located below the display window:
• Use buffer 1 as background: When this option is selected the back-
ground spectrum is measured during the TRS measurement. Other-
wise the background spectrum of the preceding measurement will be
used.
• Split Forward/Backward Interferogram: This option will split the
buffer which contains the combination of the froward and backward
scan into individual forward and backward scans. The effective result
is a doubling of the time resolution. This option can only be used
when Single Sided Forward/Backward or Double Sided Forward/
Backward was selected as Acquisition Mode.
• Split Double-Sided Interferogram: This option leads to another dou-
bling of the time resolution by splitting every double-sided interfero-
gram into two single-sided parts. This can only be used when Double

Measure
Sided Forward/Backward, Double Sided Fast Return or Double

Sided was selected as Acquisition Mode.
If both, Split Double-Sided Interferogram and Split Forward/Backward Interfero-

gram has been selected and Double Sided Forward/Backward was chosen as
Acquisition mode, four interferograms (spectra) are generated per buffer. This
represents the maximum time resolution at a given mirror velocity
Enter a description of the method you created in the Description field and store
it to disk using the Save button. Later on, you can load it (Load button) again.
The Check Syntax command helps you to locate errors in the code you created.
After you set up the Rapid Scan method you start the data acquisition from the
Basic tab by clicking on the Start Rapid Scan Measurement button. The
progress of the measurement is indicated on the status bar. If the Split Forward/
Backward Interferogram mode is used, the maximum scan count shown is
twice the number of scans specified in the measure command, i. e. the com-
mand Measure 4 scans produces 4 forward and backward scans which corre-
sponds to a total number of 8 scans.
7.5 Interleaved Time Resolved

Measurements
The electronics of several of the BRUKER spectrometers can generate up to 16

data points (equidistant in time) per standard interferogram data point. This can
be used to investigate the kinetics of rapid processes which are completely
reproducible with as many as 16 time slices. If the time needed to digitize the n
time slices is larger than the time available between two normal interferogram
data points, the time slices can be distributed over several scans (interleave fac-
tor >1).1
When selecting Interleaved Time Resolved Measurements from the Measure-

ment menu, a dialog box will open, which contains pages that are similar to the
other measurement dialog boxes described above. On the Timing/Interleave tab,
all parameters for the interleaved measurement can be entered.
1.In order to make use of the interleave values >1, the PLL (Phase Locked Loop) hardware option
is needed for laser frequency multiplication.

Direct Command Entry
Figure 89: Rapid Scan Time Resolved Measurements – Method Editor
• Time Resolution: Distance between two time slices in microseconds.

• Number of Time Slices: Number of time slices n which are to be mea-
sured per normal interferogram data point. Values between 1 and 16
are possible. n time slices will lead to n spectra.
• Trigger Delay: Delay between the trigger of a normal data point and
the digitalization of the first time slice in microseconds.
• Max. Experiment Repeat Rate: Maximum repetition rate of the mea-
surement. The actual repetition rate will be smaller than this value.
After the measurement, the data are sorted into n interferograms belonging to
the individual time slices. If desired, the corresponding single channel spectra
are computed. Similar to TRS-measurements, the results are stored in a 3D data
file.
7.6 Direct Command Entry
For testing and while using macros the direct command entry can be very help-
ful. The commands sent to the optics will be logged in a protocol and also writ-
ten in a history buffer on the screen. By clicking on a line in the history this
command line can be repeated.

Measure
Figure 90: Direct Command Entry
7.7 Optics Diagnostic
This function tests the source, laser, interferometer and the electronics. The test
result is displayed after the test is finished. The detailed result is available on the
Service tab of the Optic Setup and Service dialog.
Figure 91: Optics Diagnostic Result

Temperature Control
7.8 Temperature Control
You can use OPUS to control external equipment like a temperature-controlled

stage. In the Temperature Control box you have to specify the serial port to
which the stage is connected and the model of the thermo-sensor. If you select
Use Serial Port default settings for this device, the default port as specified in
Windows will be used. Enter the final temperature in the Set Temperature box;
press the Read Temperature button to measure the momentary Temperature of
the stage. If you automate your experiment using a macro you can halt the
macro until the stage is at the desired temperature by clicking on Wait for Tem-
perature.
Figure 92: Temperature Control – Basic Settings
The Extended Commands tab provides a window for direct command input; the
command will only be transmitted after you press the Send button. Clear pro-
vides a blank window. Save your command sequence using the Save Settings
button. You find the commands listed in the manual of your temperature control
unit. The following syntax applies:
To read a command: R <command>

To write a command: W <command>

Measure
Figure 93: Temperature Control – Extended Commands

8 Manipulate
This chapter describes all OPUS data manipulation options. The term Manipu-
late involves all arithmetic methods which modify or create new spectral data of
a spectrum acquired.
Figure 94: Manipulate Menu
The dialog boxes of the different Manipulate commands almost look like the
same. Each dialog box consists of the following tabs:
• The Select Files tab allows to select the files to be manipulated, as

Manipulate
well as to define the most important manipulation parameters. For

details, see section 2.1.
• The Frequency Range tab allows to define the spectral limits of
manipulation. For details on how to interactively select frequencies,
see section 2.7.
As the calculation results are only temporary files (work files), you need to
directly save them by using the Save File command of the File menu. If you exit
OPUS without saving the work files, the manipulation data get lost. Normally, a
warning pops up when you want to exit OPUS indicating the existence of data
which have not yet been saved.
8.1 Baseline Correction
You can perform a baseline correction for several spectra at the same time.
First, load the spectrum file you want to correct by clicking on the Load File
command in the File menu. Select Baseline Correction in the Manipulate menu.
The file name will automatically be displayed in the File(s) to Correct field.
Figure 95: Baseline Correction – Select Files
You can either accept the baseline points automatically set by OPUS, or set
them manually. Click on the Start interactive mode button. A new window
opens which shows the original spectrum on top and the baseline correction at
the bottom. Check the option button Straight lines or Polynomes to adjust
straight lines or polynomes to the baseline.

Baseline Correction
Figure 96: Baseline Correction – Interactive Mode
Double click on the original spectrum to add a baseline point. The result of this
correction will be immediately displayed in the second spectrum window. If
you want to remove a baseline point, double click on this point again.
You can also zoom spectra. Right click on the original spectrum and select the
Zoom In or Zoom Out function from the pop-up menu. For details, see
section 2.3). Click on the Store button to save the correction results.
To automatically correct the baseline of your spectrum select the Select Method
tab. A different dialog box opens and allows to specify the correction method,
e.g. Scattering or Rubberband, and the number of baseline points. Optionally,
you can exclude the spectral ranges which contain CO2 bands (between
2400 ... 2275 cm-1 and 680 ... 660 cm-1). This is only possible in case of an
automatic baseline correction.

Manipulate
Figure 97: Baseline Correction – Select Method
Specify the number of baseline points. Enter a value between 10 and 200
(except that the frequency range selected is too small). The default value is 64.
Select a correction method and start the calculation by clicking on the Correct
button.
Both baseline correction methods divide spectra in n ranges (n being the num-
ber of baseline points) which are of equal size. In the case of absorbance spectra
the minima are determined within these n ranges. The baseline points are con-
nected by straight lines. From the bottom up a rubberband is stretched over this
curve. Each baseline point which is not exactly on the rubberband is omitted.
The rubberband serves as baseline.
If you check Scattering Correction, the rubberband is created in such a way that
at each point the slope of the baseline must be negative for an absorbance-like
spectrum (provided that the spectrum is displayed in decreasing wave numbers
from left to right).
Baseline corrections can also be performed on transmittance spectra. First, max-

ima are determined in the transmittance spectrum and the rubberband is calcu-
lated. Then, the original spectrum is divided by the rubberband. You will get the
same result if you convert the transmittance spectrum into an absorbance spec-
trum, perform the baseline correction and re-convert the result spectrum into a
transmittance spectrum.
Figure 98 shows an original absorbance spectrum and a baseline-corrected

spectrum, using the Rubberband Correction method and 64 baseline points.

Baseline Correction
Rubber Band
Scattering Correction
Figure 98: Spectrum prior to and after Baseline Correction
If you subtract the corrected spectrum from the original spectrum, the baseline
can be determined, see Figure 99.

Manipulate
Figure 99: Original Spectrum and Rubberband Baseline
8.2 Spectrum Subtraction
This kind of calculation subtracts spectra, with one multiplication factor each,
from a multi-component spectrum. An additive constant can be determined. If
you click on the Spectrum Subtraction command, the following dialog opens:
Figure 100: Spectrum Subtraction - Select Files

Spectrum Subtraction
Figure 101: Spectrum Substraction - Frequency Range
The result of this calculation which can be attributed to different components is

as follows:
Result spectrum (ν) = multi-component spectrum(ν)
– Factor1 * single-component spectrum (ν)
– Factor2 * single-component spectrum (ν)
...
– Offset
Note: This kind of calculation is only appropriate for absorbance spectra. Trans-
mittance spectra are automatically converted to absorbance spectra during calcu-
lation. Only if the original spectrum has been of transmittance mode, the resulting
spectrum will be converted to transmittance when the subtraction has been fin-
ished.
Example:
First, generate an example spectrum using the Spectrum Calculator. The spec-
trum has to consist of 0.7 ABBOE12.0 spectrum parts, 1.3 ABBOE08.0 spec-
trum parts and 2.3 ABBOE05.0 spectrum parts (see chapter 8.5). Save the
spectrum as CALC.6. This spectrum should represent a generic sample consist-
ing of an unknown amount of these three components and be analyzed by using
Spectrum Subtraction. The automatic subtraction mode minimizes the least
squares deviation in the difference spectrum.

Manipulate
The optimum result can only be achieved if all single components are simulta-
neously subtracted from one mixture spectrum. This yields to a result of almost
zero.
If you click on the Start Interactive Mode button, the following dialog box will
be displayed:
(a)
(b)
(f)
(c)
(d)
(g)
(e)
Figure 102: Interactive Spectrum Subtraction
a) Shows the name of the multi-component spectrum.

b) If you click on the drop-down list, you can select the spectra to be subtracted.
c) Depending on your spectra selection in (b), the adjusted factors are displayed.
The factor value can be increased or decreased, using the control elements on the
right. The value can also be entered manually. Click into the entry field and
overwrite the value given.
d) If you check this option, the displayed spectra will be scaled.
e) Use this slider to define the number of decimals which vary the components of
(c).
f) This window shows both the single-component spectra and the multi-component
spectrum.
g) The display is autoscaled and shows the difference between the multi-component
spectrum and the weighted single-component spectra.
If you right click into the windows (f) and (g), you can zoom in specific spectral
ranges using the pop-up menu. The Auto Subtract button would start the auto-
matic single-component subtraction. If you click on the Store button, you exit
this dialog box and the difference spectrum is stored as Principal File (a).
The numerical values used are attached to the spectrum in the form of a subtrac-
tion data block . This data block contains the factors used to subtract the
spectra and the result spectrum. If you right click on the subtraction data block,
the Show Report option pops up. Select this option to open the report window:

AB <-> TR Conversion
Figure 103: Spectrum Subtraction Report
The first column on the right shows the factors and the mark in the Modified
column indicates the spectrum which the subtraction report has been attached
to.
8.3 AB <-> TR Conversion
This function converts absorbance spectra to transmittance spectra and vice

versa. The conversion direction can be set automatically, or individually pre-
defined.
Figure 104: AB <-> TR Conversion
If you definitely determine a conversion direction, only those spectra will be

converted which do not have the requested format. This Conversion Direction
option allows to create a uniform data block type for several spectra. Click on
the Convert button to start conversion.

Manipulate
Figure 105: Converted Absorbance Spectrum into a Transmittance Spectrum
The spectrum displayed by a dotted line can be generated if you convert the
absorbance spectrum into a transmittance spectrum.
The equation used for TR <-> AB conversion is:
AB = – log ( TR )
Transmittance values below 10-5 are set to 5 absorbance units.
The equation used for AB <-> TR conversion is:
TR = 10 – AB
8.4 Straight Line Generation
This function allows to eliminate fringe effects in the interferogram or artifacts

detected in a spectrum. Click on the Straight Line Generation command in the
Manipulate menu. Select the spectrum files and define the frequency range in
the Straight Line Generation dialog box. You can either select the frequencies
interactively, manually or accept the current frequency limits of the spectrum.
When you have finished setting the frequency limits, click on the Generate but-
ton.

Spectrum Calculator
Figure 106 shows a straight line generated between 2,550 and 2,360 wave num-
bers, which replaces the original peak (dotted line).
Figure 106: Spectrum Before and After Generating a Straight Line
8.5 Spectrum Calculator
The Spectrum Calculator is used to calculate spectra and numerical results. You
can also enter algebraic terms.

Manipulate
(a)
(b)
(c)
(d)
(h)
(e)
(i)
(f)
(j)
(g)
Figure 107: Spectrum Calculator
a) Use the Backspace button to delete your input.

b) The cos button provides trigonometric functions. The following functions are available if
you use the Shift and Hyp button:
c) Additional mathematical functions, e.g. square function 2 (e.g. 32 = 9) and “^”, as well as
π and special function x are made available.
sqrt is the square root function √
ln is the natural logarithm
lg is the logarithm to the base 10
exp is the exponential function e
dxp takes the following entry to the power of x (i.e. 10x)
d) C clears the display (h) and (i). You can use the brackets ( ) to form mathematical groups
that will be calculated first.
e) The four basic arithmetic operations.
f) Numerical block which consists of the figures 0 - 9, the decimal point and exponential
function E (e.g. 4.321E3 = 4321).
g) This button starts the calculation. The result will be displayed in the entry field (h).

Cut
h) You can drag & drop spectra from the OPUS browser window to entry field (h). They are
directly made available for mathematical calculations. You can also enter algebraic terms
and numerical values into this entry field.
i) Select the result data block from the drop-down list.
j) The display field shows the calculation results or indicates ERROR in case of an incor-
rect entry.
You can enter figures, signs and functions either using the numerical keypad of
your keyboard or clicking on the spectrum calculator keys. In the latter case
inputs will always be added to the entry field (h). Delete inputs using the Back-
space button.
If the calculation results in a spectrum, the original spectrum file will be over-
written by the new result spectrum. This also applies to data blocks.
If two spectra are divided, a transmittance spectrum is generated in the numera-

tor of these two spectra. The transmittance spectrum may overwrite the original
spectrum.
In some cases it may be necessary to calculate frequency-dependent terms. This

can be done using the x function, which represents the frequency values of the
spectral data points. The term
sin(x/100) + [4:TR] – [4:TR]
uses the group ([4:TR] – [4:TR]) to generate a spectrum with zero intensity. The
x function causes the frequency limits and data point (frequency) spacing to be
applied. The result will be a sine wave. If you calculated
sin (x/100) + [4:TR], the spectrum intensity values would be added to the sine
wave.
The spectrum calculator cannot be compared with a normal pocket calculator. If

you enter 100√ into the pocket calculator you expect the result to be 10. The
spectrum calculator, however, operates with algebraic formulae. Therefore, you
need to enter sqrt(100).
It is also possible to use the spectrum calculator in case of 3d data. For details,
see 3D/VIDEO manuals.
8.6 Cut
Use the Cut command to minimize the frequency range of a data file. The Cut
dialog box opens. Select the spectrum and define the frequency range. Click on
the Cut button to start the function. Figure 108 shows a frequency range (thicker
curve line) generated by using the Cut function.

Manipulate
Figure 108: Original Spectrum (Thin Line) and Cut-Out Range (Thick Line)
You can also use the Cut function to invert the frequency limits of spectra.
Select upper and lower limits which are beyond the spectral range and define
them as new frequency limits in reverse order. Right click on the spectrum and
select Properties from the pop-up menu. Invert the axes settings using the Axes
tab. This change may not immediately appear in the spectrum window.
8.7 Normalization
The Normalization function allows to normalize spectra and perform offset cor-
rections on spectra. Click on the Normalization command. Three different
methods are available for spectrum normalization:

Make Compatible
Figure 109: Normalization
• Min/Max normalization – This method scales spectrum intensities to

the effect that the minimum absorbance unit will be 0 and the max-
ium 2. In case of transmittance spectra the normalization is between
0 and 1.
• Vector normalization – This method calculates the average y-value
of the spectrum. The average value is subtracted from the spectrum
decreasing the mid-spectrum to y = 0. The sum of the squares of all
y-values is calculated and the spectrum is divided by the square root
of this sum.
NPT 2
The vector norm of the result spectrum is 1: ∑ ( xi )
i=1
= 1
Offset correction – This method shifts spectrum intensities to the effect that the
minimum absorbance unit will be 0.
8.8 Make Compatible
The Make Compatible function changes the data point grid of the selected files
to adapt it to the Principal File grid. The files to be processed are manipulated
to make the x-values of the spectra compatible to those of the principal file. This
causes the frequency base points to be shifted. If the frequency range of a spec-
trum selected is larger than the range of the Principal File, the frequency range
will be cut. Many OPUS functions make spectra automatically compatible to
each other.

Manipulate
Figure 110: Make Compatible
There are two methods to calculate the intensities of new frequency base points.
The original intensities serve as a basis.
• Interpolation – The method of quadratic interpolation can always be

used.
• Reduce Resolution – The new intensities are calculated by integrat-
ing the original ones.
In case of the Interpolation method the curve shape is better preserved, while
Reduce Resolution keeps the peak positions more constant.
Example:
The frequency limits of the Principal File are between 1,000 and 5,000 cm-1.
The number of data points is 4,001 (i.e. 1 cm-1 resolution). The frequency of the
first point is 4,000.5, of the last 200.5 cm-1. The number of data points is 1,901
data points (2 cm-1 resolution). The Make Compatible function creates a new
spectrum on the basis of the original one. The first frequency point of this new
spectrum is at 1,000 cm-1 and the last one at 4,000 cm-1. The number of data
points is 3,001 (1 cm-1 interpolated resolution).
The x-direction (high-to-low or low-to-high) of the new spectrum always

depends on the Principal File.

Convert Spectra
8.9 Convert Spectra
This function performs several data conversions which mainly involve the
y-axis. When selecting spectra for conversion certain restrictions may apply. If
you try to select a spectrum which does not comply with the conversion method
selected, a warning symbol will be displayed. The file name in the File(s) to
Convert field of the Select Files tab will be red.
Figure 111: Convert Spectra – Mismatch of Method and Spectrum
Define the spectrum and frequency range, select a conversion method and click
on the Convert button to start the function.
8.9.1 Convert to Kubelka-Munk

The Kubelka-Munk conversion type is designed for spectra which are measured
in diffuse reflectance. In case of Kubelka-Munk units the spectral intensities are
more linear to concentration than absorbance units.
KM = (-------------------------
1 – Refl ) 2-
( 2 ⋅ Refl )
Rfl also means TR in this case. Absorbance spectra are first converted to trans-
mittance spectra. The smallest value allowed for transmittance is 0.001%. This
corresponds to a Kubelka-Munk value of about 500.

Manipulate
8.9.2 Convert to Reflectance Spectra

The following conversion formula is applied:
Refl = 1 + KM – ( 2 ⋅ KM + KM 2 )
8.9.3 Convert to ATR Spectra

X
ATR = AB ⋅ ------------
1000
X represents the wave number. Transmittance spectra are first converted to

absorbance spectra. In Attenuated Total Reflection measurements the penetra-
tion depth is inversely proportional to the wave number (frequency). The spec-
tra are normalized to a constant penetration depth using ATR units.
8.9.4 Convert to Absorbance Spectra
1000
AB = ATR ⋅ ------------
X
8.9.5 Logarithmize Reflectance Spectra

Spectra reflectance values below 0.00001 will be levelled to a lg(Refl) intensity
of 5.
logRefl = -log(Refl)
8.9.6 Convert Logarithmized Reflectance Spectra

R = 10 –log ( R )
8.9.7 Convert Single-Channel Spectra

The start and end frequencies of a single-channel Raman spectrum will be con-
verted using the following equations:
FXV ( Raman ) = RLW – FXV ( ScSm )

LXV ( Raman ) = RLW – LXV ( ScSm )
RLW stands for Raman Laser Wave number. This value is registered within the
instrument parameter block of the Raman file created. OPUS uses ScSm to indi-
cate a single-channel spectrum (single-channel sample). FXV represents the
starting frequency, LXV the end frequency.

Atmospheric Compensation
8.9.8 Convert Raman Spectra

The equation used for the conversion is:
FXV ( ScSm ) = RLW – FXV ( Raman )
LXV ( ScSm ) = RLW – LXV ( Raman )
The RLW parameter belongs to the instrument parameter block of the Raman
spectrum.
8.9.9 Raman Laser Wave Number

This value will be used for the ScSm → Raman conversion.
8.10 Atmospheric Compensation
This function eliminates disturbing H2O and/or CO2 bands in the ratio spectra.
These bands arise due to different H2O/CO2 vapor concentrations in the beam
path when measuring reference or sample spectra.
To perform Atmospheric Compensation a single-channel reference and single-

channel sample spectrum are analyzed and transformed into a ratio spectrum
without any (or as few as possible) H2O and/or CO2 bands.
Select the Atmospheric Compensation command from the Manipulate Menu.

The following dialog box opens:

Manipulate
Figure 112: Atmospheric Compensation - Select Files
8.10.1 Selecting spectra

The Atmospheric Compensation function uses two single-channel spectra and
produces one ratio spectrum. Drag the single-channel sample spectra into the
Single-channel Sample block(s) field, and the reference spectra into the Single-
channel Reference block(s) field.
If you want to simultaneously compensate several ratio spectra, be careful not to

mix up the two single-channel spectra which belong together.
8.10.1.1 Single-channel sample and single-channel refer-

ence spectrum in one file
If the single-channel sample and single-channel reference data block of the
spectrum are stored in one file, select the files and drag and drop them into each
one of the two selection fields within the Select Files tab. Only correct types of
data blocks will be accepted (see Figure 112).
If you have selected several files, a data block will be displayed for each file in
each selection field.

8.10.1.2 Single-channel sample and single-channel refer-

ence spectrum in different files
If the single-channel sample and single-channel reference data block of the
spectrum are stored in different files, select the single-channel reference spec-
trum and drag and drop it into the Single-channel Reference block(s) field. Drag
and drop the single-channel sample spectrum into the Single-channel Sample
block(s) field.
If you want to simultaneously correct several spectra, make sure you have as
many single-channel sample spectra and one-single channel reference spectra as
depicted in Figure 113.
Figure 113: Atmospheric Compensation - Single-Channel Spectra in Different Files
8.10.2 H2O/CO2 Compensation
You can define the atmospheric gas you want to use during compensation. If
you uncheck both boxes, you will get an uncompensated transmission spectrum,
i.e. the ratio of a single-channel sample and single-channel reference spectrum.
Activate the Aqueous solution checkbox if your measurement sample is an
aqueous solution (e.g. proteins in water). A different compensating algorithm
optimized for aqueous solutions will be performed.

Manipulate
8.10.3 Calculate
Click on the Calculate button to start the Atmospheric Compensation. For each
single-channel sample block the appropriate transmission block will be calcu-
lated and added to the original spectrum file.
If a transmission block already exists, it will be overwritten by the latest one.

Figure 114 shows the Atmospheric Compensation effect.
Figure 114: Atmospheric Compensation Effects
The upper curve is the transmission spectrum of a polystyrene film. H2O and
CO2 bands can be clearly seen in several wave number ranges. The lower curve
is the result of atmospheric compensation. Disturbing absorption lines of H2O
and CO2 have almost been completely eliminated.
8.10.4 Requirements
• Single-channel spectra have to include wave number ranges starting

from 3600 to 4000cm-1 for H2O compensation, and
2300 to 2400cm-1 for CO2 compensation.
• Sample absorption within these wave number ranges will result in
poorer quality with regard to compensation.
• The sample and reference spectrum have to be acquired by using the
same spectrometer resolution. Different zero-filling factors are possi-
ble.

• The spectrum should not end at a wave number which shows strong
absorption of atmospheric gases. To get an adequate H2O-compensa-
tion in the above example, the lower wave number limit must not be
around 1700 cm-1.
• For compensation in aqueous solutions the wave number ranges need
to be within 2300-2400 cm-1 and 1800-1900 cm-1 for both CO2 and
H2O.
• These wave number ranges must be free of sample absorption bands.
8.10.5 Limits
The Atmospheric Compensation feature uses physical models to estimate the
amount of atmospheric gases in the single-channel spectra and therefore com-
pensates disturbing H2O and/or CO2 bands. This kind of spectral manipulation
option modifies original data and has to be used with due care.
8.10.6 Atmospheric Compensation as part of the

measurement process
If you want to use Atmospheric Compensation to manipulate spectra immedi-
ately after the measurement process, you have to perform the following steps:
1) Select the Advanced Measurement command in the Measure menu and
set the parameters for your experiment. Click on the Advanced tab.
2) Activate the Single Channel and Background checkboxes in the Data
blocks to be saved option field.
3) Check Additional Data Treatment and click on the button.
4) The following window pops up:
5) Select Atmospheric Compensation from the Manipulate menu. The

Atmospheric Compensation dialog box opens.

Manipulate
Figure 115: Atmospheric Compensation - Select Files
6) Select [<FILE>:ScSm] from the Single channel Sample block(s) drop-

down list and [<FILE>:ScRf] from Single channel Reference block(s)
drop-down list. Activate the different checkboxes, if required.
7) Click on the Calculate button.
The Advanced tab of your Measurement dialog may be similar to Fig. 116. If
the sample measurement has been successful, additional spectra manipulation,
e.g. Atmospheric Compensation will be performed immediately.

Straylight Correction
Figure 116: Measurement - Activated Post-Measurement Manipulation
8.11 Straylight Correction
This function allows to correct two phenomena which normally occur in case of
diffuse reflection measurements:
1) Diffuse reflection of the incoming light at the window, mainly due to
scratches and contaminations.
2) Multiple reflections between sample and window, which lead to
increased absorption.
To perform Straylight Correction one or more ratio spectra (i.e. transmission,

absorbance, Kubelka-Munk, reflection) are recalculated using intrinsic correc-
tion spectra which will produce corrected ratio spectra.
Select the Straylight Correction command from the Measure menu. The follow-
ing dialog box opens:

Manipulate
Figure 117: Straylight Correction - Select Files
8.11.1 Selecting spectra

Drag and drop the desired spectra files from the OPUS browser window into the
Spectra to apply straylight correction field. Only ratio blocks, e.g. absorbance,
transmittance, Kubelka-Munk, reflectance or log-reflectance will be accepted.
8.11.2 Window material

The correction of multiple reflections depends on the refraction index of the
window material. To specify the material, activate either the Quartz or Sapphire
checkbox.
8.11.3 Internal background

Activate or deactivate the Internal background was used checkbox to specify
whether your reflection measurement has been performed by an internal or
external background. External means you have used your own standard, e.g. a
gold stamp or certified Labsphere standard, which you place on the measure-
ment window during background measurement.

Internal means you have used built-in features of the Ulbricht sphere to deter-
mine the background spectra (i.e. Sphere Background-Channel in case of an
MPA spectrometer).
8.11.4 Calculate
Click on the Calculate button to start Straylight Correction. The ratio spectrum
will be calculated for each ratio block which is displayed in the Spectra to apply
straylight correction field. The ratio block will be overwritten by the calculation
result.
The correction algorithm considers three effects:

1) Straylight effects caused by diffuse reflection of the incoming light at
the measurement window. This will be corrected by calculating a cor-
rected ratio spectra:
TM − Stray
TM corrected = If TM has been recorded using an inter-
Extref − Stray nal background.
TM − Stray / Extref If TM has been recorded using an

TM corrected =
1 − Stray / Extref external background (nearly
100%).
TM is the original Transmission, TMcorrected the resulting spectrum.

Stray means transmission spectrum of a measurement without sample
(open channel), i.e. totally absorbing material. Extref is the ratio
between the single-channel spectra of the external reference and single-
channel internal background.
2) Effects caused by multiple reflections between the measurement win-
dow and sample. After the first diffuse reflection of the light at the sam-
ple, a fraction of this light can be reflected again both by the window
and the sample. This leads to incorrect measurements especially in case
of a mid-range sample absorption ratio (30-70%). This effect is compen-
sated by multiplying the transmission spectrum by the following factor:
1+ c (
c = R ⋅ 1 + (1 − R )
2
)
1 + TM ⋅ c where
and TM is the original transmission spectrum.

3) Effects produced by using an internal background instead of an external
standard.
The difference between internal and external background is the portion
of light reflected directly at the measurement window. The light leaves
the Ulbricht sphere by the input. This effect is taken into account by a
correction spectra which quantifies this background difference.

Manipulate
Figure 118 shows straylight correction effects.
Figure 118: Straylight Correction Effects
As the straylight effect is taken into account when calculating reflection spectra,
the relative change, especially in low-reflection wave number ranges, substan-
tially increases.
8.11.5 Create new correction spectra

Each OPUS release includes a set of correction spectra which can be used for
straylight correction. It is, however, important that these spectra reproduce the
properties of your spectrometer. Therefore, it is recommended to create your
individual set of correction spectra before using the OPUS Straylight Correc-
tion function. Spectra should be frequently created (e. g. each month).
To proceed sucessfully you need a standard material, e.g. gold standard or certi-
fied Labsphere standard (99%). Without a standard being available it is possible
to create new correction spectra but not reasonable, because you may obtain
correction spectra which represent the actual amount of straylight worse than
default spectra. The correction algorithm assumes that the standard used has a
diffuse reflection of about 100% within a wave number range of 15000 to
3000 cm-1.

To create new correction spectra, click on the Create new correction spectra
button. A new dialog box opens. Follow the on-screen instructions. If you have
finished, the new correction spectra will be automatically saved on hard disk.
The Straylight Correction function always uses the latest correction spectra cre-
ated.
8.11.6 Using straylight correction as part of the

measurement process
If you want to use Straylight Correction to manipulate spectra immediately
after the measurement process, you have to perform the following steps:
1) Select the Advanced Measurement command in the Measure menu and
set the parameters for your experiment. Click on the Advanced tab.
2) Use the Result Spectrum drop-down list to define the result spectrum
type. This type has to be one of the following: Transmittance, Absor-
bance, Kubelka-Munk, Reflectance or Log Reflectance.
3) Activate the Single Channel and Background checkboxes in the Data
blocks to be saved option field.
4) Check Additional Data Treatment and click on the button.
5) The following window pops up:
6) Select Straylight Correction from the Manipulate menu. The Straylight

Correction dialog box opens.

Manipulate
Figure 119: Straylight Correction - Select Files
7) Select the result spectrum, e.g. [<FILE>:TR] from the Spectra to apply
straylight correction drop-down list. Activate the checkbox and radio
buttons, if required.
8) Click on the Calculate button.
The Advanced tab of your Measurement dialog may be similar to Fig. 120. If
the sample measurement has been successful, additional spectra manipulation,
e.g. Straylight Correction will be performed immediately.

Noise generation
Figure 120: Measurement with Activated Post-Measurement Manipulation
8.12 Noise generation
This function adds noise to a spectrum. It adds random positive or negative

numbers to the spectrum values. In the Noise level entry field you determine the
degree of spectrum noise, i.e. the higher the Noise level the higher the noise fre-
quency of the spectrum. Select a spectrum file and click on the Noise generation
command. The following dialog box opens.

Manipulate
Figure 121: Noise Generation - Select Files
Click on Generate to start this manipulation option.
8.13 Moving Mean
Moving Mean performs some kind of smoothing on a spectrum. Select a file and
click on the Moving Mean command. The following dialog box opens:

Moving Mean
Figure 122: Moving Mean - Select Files
Two different kinds of manipulation are possible. In both methods the Number
of points parameter always represents the number of subsequent spectrum
points. These spectrum points are used for the calculation to be able to create
new spectrum values.
If you check Calculate moving mean, spectrum values being next to each other
are averaged over and replaced by their mean value. If you check Calculate
moving slope, the first and the last data point of a sequence are used to calculate
a straight line between these two data points. The spectrum points between
these two data points are replaced by values determined on the straight line.
These steps are repeated using the next sequence of data points. The number of
data points are defined in the Number of points entry field.
Click on the Calculate button to start this manipulation function.

Manipulate
8.14 Make Monotone
Depending on the options selected and the spectrum curve shape, the Make
Monotone function forces a spectrum to increase or decrease in a monotonic
manner. Select a file and click on the Make Monotone command.
Figure 123: Make Monotone - Select Files
You can select between three manipulation directions. If you check Upwards,
the spectrum values will be changed to the effect that the resulting spectrum
values increase in a monotonic way. If you check Downwards, the resulting
spectrum values will decrease in a monotonic way.
Automatic tries to automatically determine whether the resulting curve

increases or decreases, considering two data points at the boundary of the wave
number interval.
8.15 Smooth
This function allows to smooth spectra. The smoothing is based on the Sav-
itzky-Golay algorithm. Possible values for smoothing points are between 5 and
25.

Smooth
Figure 124: Smooth – Select Number of Points
Select the file, define the number of smoothing points and click on the Smooth
button to start the function. It is also possible to click on the Start interactive
mode button.
Figure 125: Interactive Smoothing

Manipulate
Figure 125 shows the original spectrum in the upper window and the smoothed
spectrum in the lower. Use the slider to set the smoothing points. If you click on
the Store button, the loaded spectrum file will be changed. You can close the
window by clicking on Cancel. In this case the changes will not be stored.
Smoothing has a cosmetic effect on the spectrum. It reduces the noise and dis-
torts the signal intensities. Figure 126 shows a spectrum smoothing effects on
the data. The original data always shows more pronounced peaks than the
smoothed one.
After Smoothing
Before Smoothing
Figure 126: Effect of Smoothing on a Spectrum
8.16 Derivative
This function calculates the first to fifth derivative of a spectrum, using the Sav-
itzky-Golay algorithm. This algorithm allows a simultaneous smoothing of the
spectrum. The smoothing effect reduces the noise generated by derivation. The
minimum number of smoothing points depends on the derivative order. The
higher the derivative order, the more smoothing points need to be set. You can
set a maximum of 25 points.

Frequency Calibration
Figure 127: Derivative
Select a spectrum file, define the number of smoothing points and the derivative
order. Click on the Process button to start.
As a result, a data block is generated indicating the actual derivative order of the
original spectrum. If a spectrum of 1st order is subject to a first-order derivation
again, the result will be a 2nd order spectrum. The kind of derivative order is dis-
played in the data block of the resulting spectrum.
First and second-order derivations are symbolized as n derivation. The deriva-

tive order is stored in the parameters of the derivation data block. Double click
on the data block to have a look on these parameters.
8.17 Frequency Calibration
This function re-calibrates the x-axis of a spectrum including. The new axis is
calculated using two parameters M and A to. These parameters change all νold
x-values of the data points. The formula is:
νnew = νold⋅M + A or fnew = fold⋅M + A
Select a spectrum and click on the Frequency Calibration command to start cal-
ibration.

Manipulate
Figure 128: Frequency Calibration
After the calibration the parameters can be found in the spectrum data block.
This gives you the possibility to undo the calibration.
The original data set before the calibration looked as follows:
Figure 129: Original Set of Data Parameters
After the calibration the frequencies of the first and last data point have
changed. Two additional parameters Mult. for Freq. Calib. and Add for Freq.
Calib. have been included in the list.

Raman Correction
Figure 130: Set of Data Parameters after Frequency Calibration
The x-axis of a spectrum can be modified several times as follows:
νold,1 = νold⋅M1+A1
and later by
νnew,2 = νnew,1⋅M2+A2
For the first run select the parameters M1 and A1, and for the second the param-
eters M2 and A2. The parameter list displays the parameters Mtotal and Atotal,
which represent the total change compared to the original calibration:
νnew,1 = νold⋅M1 + A1
νnew,2 = νnew,1⋅M2 + A2
νnew,2 = νold⋅Mtotal + Atotal
⇒(νold⋅M1 + A1)⋅M2 + A2 = νold⋅Mtotal + Atotal
⇒Mtotal = M1⋅M2
Atotal = A1⋅M2 + A2
These changes can be reversed in just one step.
8.18 Raman Correction
The special features of the optics and the frequency dependent scattering that
occur in Raman spectra can almost be eliminated by using the Raman Correc-
tion option. To undo the Raman Correction, check the Restore Original Data
option.

Manipulate
Select a spectrum file, only Raman spectra, and click on the Raman Correction
command.
Figure 131: Raman Correction
The Correction Method tab allows to define the correction method and the ref-
erence spectrum which is to be used as well as the temperature. If you check the
Reference Correction option, you correct the influence which the optics has on
the spectrometer. This requires a current spectrum of the reference lamp
installed in the sample compartment. The spectrum should not be older than two
weeks to reflect the aging of the lamp. The correction spectrum (almost similar
to the one acquired by Black Body) can be selected if you click on the Change
Reference File button. If the sample spectrum and the reference lamp spectrum
do not match in your data point grid, click on the Make Compatible command of
the Manipulate menu. Scatter Correction corrects the dependence between scat-
tered radiation and excitation frequency.
Click on the Correct button to start the correction. The correction parameters
are stored in the Instrument parameters list:
Figure 132: Raman Correction Flags
Thus it is avoided that the same correction is used several times. Ensure that the
Raman laser wave number and the source temperature have not changed just
before performing the correction.

Black Body
Theory:
Rayleigh's υ4-law relates the scattering as a function of the wave number. The
effect increases with the spectral distance of the line of interest to the wave
number of the Raman laser. In case of Scatter Correction the Raman spectrum
is multiplied point by point using:
υ
4
Laser
--------------
-
 υ 
In case of the Reference Correction the point-to-point multiplication for the

Raman spectrum to be corrected will be as follows:
(-------------------------------------------------------------------------------------------------------
Black Body Spectrum ) ( Raman Spectrum -)
( Reference Spectrum )
8.19 Black Body
This function calculates the radiance spectrum of a black body on the basis of
an existing measured spectrum. The frequency region and data point spacing, as
well as the units of the x-axes will be taken from the single channel spectrum.
Removal of the wave number dependence of the instrumental light throughput
in emission and Raman spectra can be performed when the true spectrum is
known or well approximated. The temperature of the light source will be given
in Kelvin and is stored (TMP parameter) together with the computed distribu-
tion.
In the case of Raman spectra, the x-axis is shifted and switched so that the
Raman laser signal is at zero and the Stokes region of the spectrum is in positive
wave numbers. The Raman laser frequency is taken from the parameter “RLW”
of the experimentally determined spectrum or can be set manually to 9394 cm-1.

Manipulate
Figure 133: Black Body Radiation
Select a file and indicate the temperature of the black body; choose the type of
distribution to be calculated and click on Calculate to start the computation.
Theory:
The radiative properties of a black body are only governed by its temperature.
This makes an approximation of the true spectrum of the light source possible
assuming that a single channel spectrum of the light source is available.
Figure 134 shows the radiation spectrum of a black body at a temperature of
1000 K.

Interferogram to Spectrum
Figure 134: Radiation Emitted by a Black Body at 1000 K
You can calculate either the radiance or the photon flux.
8
Radiance: 2 ×10 hc 2 ν 3-
y = -----------------------------
 100νhc
------------------
 kT 
e –1
– 15
Photon flux: 2 ×10 cν 2-
y = -----------------------------
 100νhc
------------------
 kT 
e –1
where:
T = Temperature [K]
c = 2.99792458⋅108 [ms-1]
h = 6.626176⋅10-34 [m2kgs-1]
k = 1.380662⋅10-23 [m2kgs-2K-1]
ν = Wavenumber [cm-1]
8.20 Interferogram to Spectrum
This function calculates a spectrum from an interferogram and thereby performs

the same steps that are usually done immediately after data acquisition, namely:

Manipulate
• Apodization
• Phase computation
• Zerofilling
• Fourier Transformation of the interferogram
• Phase correction
This function is helpful for transforming interferograms after measurement by

allowing different parameters to be used for apodization, phase correction and
zerofilling. The input data has to be an interferogram and the values should lie
between the High folding limit and the Low folding limit parameters used during
the measurement (which can be obtained from the instrument parameter block
of the interferogram).
Figure 135: Interferogram to Spectrum – Store
Select the spectrum on the first tab of the dialog box. On the second tab specify
the frequencies and the spectrum type to be saved. In addition to the calculated
spectrum block (which always is of type “Single-Channel”), one can also save
the Phase spectrum and the Power spectrum. They can be calculated from the
parts of the interferogram known from forward and backward scans with the
Phase Resolution setting.

Figure 136: Interferogram to Spectrum – Apodization Tab
Because of the finite mirror travel, the interferogram data are only measured up
to a certain point (i.e. a finite resolution). This leads to artificial side lobes on
spectral lines whose natural width is smaller or comparable with the measured
resolution. By multiplying the interferogram with an apodization function, these
side lobes can be reduced but at the cost of line broadening.
Choose an appropriate function on the Apodization tab. For standard measure-

ments in liquid or solid phases, the Blackman-Harris-3-term is recommended.
To obtain the highest resolution, choose no apodization (Boxcar) or if necessary
a weak apodization (Norton-Beer-weak).
Zero filling is the adding of zeros to both ends of the interferogram before the
Fourier transformation. It results in an increased number of points in the spec-
trum (which corresponds to an interpolation). The zero filling is input as a factor
(2, 4, 8,..., 512) which increased the number of spectrum points from the mini-
mum (1) to the specified value. The more data points in the spectrum, the better
looking sharp lines become (cosmetic effect). However, this requires n-times
the computing time and n-times storage space.
For single-sided interferograms a minimum factor of 2 is required. For double-

sided interferograms, the zero-filling factor can be halved in comparison to sin-
gle-sided collections.

Manipulate
Figure 137: Interferogram to Spectrum – Limit Data
If the box Limit Resolution is checked, one can vary the resolution by entering a
“Resolution Limit” that is larger than, or at least equal to the value used in the
measurement. Then only a fraction of the measured interferogram is used.
The Phase Resolution is the resolution for computing the phase. Normally the
same resolution as was used for the measurement should be used.
Interferograms recorded in forward/backward mode can be processed using

either the scans during the forward or the backward movement of the mirror. If
both mirror travels should be evaluated, the forward and the backward scans
will be transformed separately, followed by a phase correction and the calcula-
tion of the average spectrum.
If the data have been recorded in multiplex mode, then the interferogram con-
tains alternating data from two ADCs. With the options even and odd the data
from both ADCs can be evaluated separately. There is no such option for back-
ward scans. Therefore, multiplex measurements should be recorded only with
pure Forward modes.
By selecting even the data indexed by even numbers I0, I2 ... will be trans-
formed, while odd transforms data indexed by odd numbers I1, I3 ...

Figure 138: Interferogram to Spectrum – Phase Correction
The phase correction can be thought of as symmetrizing the interferogram

which is always necessary due to the asymmetry of any measured interfero-
gram. Several phase correction methods are available:
• Mertz: this is the standard procedure.
• Mertz signed: modified Mertz function is used if the single channel
spectrum is expected to contain negative contributions.
• Power spectrum: This can be used instead of Mertz or Foreman, but
only for double-sided interferograms, when the spectrum has wide
ranges of low light intensity (e.g. total absorption, Raman, emission).
Disadvantage: up to √2 more noise compared with Mertz or Forman.
• Mertz/Stored Phase: like Mertz, but the phase won’t be calculated
and will instead be taken from previously existing data for which the
phase was obtained using the regular Mertz method. This can be use-
ful for example, if the maximum of the interferogram is not very well
defined, as e.g. for emission or Raman measurements. Also, if the
spectra are expected to contain parts with negative contributions. In
this case, the phase information used should be taken from a spec-
trum with only positive values.
• No/Save complex data: the data will not be phase corrected but is
instead transformed in complex form and stored as with real and
imaginary parts.
• Forman: a method mathematically equivalent to Mertz, offers a
slightly higher precision at the cost of higher computational costs.
• Doubled Phase:

Manipulate
Figure 139: Non-linearity Correction
In a single-channel spectrum there should be no signal below the absorption

cut-on of the detector. The non-linear detector response causes the signal to be
non-zero in these regions. The non-linearity of the detector can be calculated
from the ratio of the intensity of these artifacts and the total energy flow in the
detector. Once the non-linearity is known, a corrected spectrum can be calcu-
lated. As a rule, the stored interferogram is not modified. The non-linearity cor-
rection (NLC) works only on such unmodified interferograms.
For a successful NLC the following prerequisites must be satisfied:

• Starting at zero wave numbers the spectrum must be recorded to the
maximum wave number where the detector can record a signal.
• Electronic filters may not be used to limit the detector response.
Spectra must be recorded broad band to avoid aliasing.
• The FT parameter Phase resolution should be set to result in at least
500 phase interferogram points. A too low phase resolution results in
an inaccurate NLC.
The NLC coefficients are calculated after the phase correction, using all the data
points of the single channel spectrum.
The modulation efficiency causes another multiplicative correction of the spec-

trum. It can be set either to the correct value (typically between 0.5 and 1.0), or
to 1.0 if it is not known. If a preamplifier is used which flips the signal polarity,
the value of the detection limit has to be multiplied by -1.
On the Peak Search tab you have the option of how to select the position of zero

Inverse Fourier Transformation
path difference (ZPD):

• Absolute largest value finds the peak with the highest absolute inten-
sity.
• Maximum finds the highest peak with the largest positive value.
• Minimum looks for the peak with the largest negative value.
• Mid between Min./Max. calculates a value halfway between the min-
imum and the maximum.
• No peak search uses the position saved in the interferogram; if this
value is known, it can also be entered manually.
Figure 140: Peak Search – Showing Zero Path Difference Settings
The position of the reference point can be influenced by including data points in
addition to those chosen by the algorithm. Every point will be tested for its sym-
metry; the point with the highest symmetry will be chosen as the ZPD. Whether
or not symmetry or antisymmetry is to be tested, can also be specified.
8.21 Inverse Fourier Transformation
This function transforms a spectrum back to an interferogram. It can be used

with all types of spectra. You have to specify whether the measured interfero-
gram originally was a symmetric or an antisymmetric one. In most cases you
should choose a symmetric transformation, because most of the spectra were
obtained involving a phase correction. The antisymmetric inverse Fourier trans-
formation should only be applied to complex spectra, e.g. spectra also contain-
ing the imaginary part.

Manipulate
Figure 141: Inverse Fourier Transform
Select the file and frequency range as usual and specify the symmetry. Start the
processing by clicking on the Inverse FT button.
8.22 Post-Zerofilling
By using post-zerofilling you can increase the number of points in the spectrum,
thus corresponding to an interpolation. This yields better line shapes (smoother)
for spectra measured with high resolution. During the Fourier transformation a
zerofilling is automatically carried out over the whole spectral range. However,
this increases the total size of the data file. Using post zerofilling allows you to
apply the interpolation once again for only the frequency range of interest,
which keeps the size of your files small. You have to specify the zerofilling fac-
tor, i.e. a factors ranging from 2 to 512. A zerofilling using a factor of 2, for
example will double the number of spectrum points by interpolation. However,
zerofilling should not be confused with an increase in spectral resolution.

Post-Zerofilling
Figure 142: Post Zerofilling
Specify the file on the first tab and select on the second tab of the dialog the
range which will be processed.
Example 1
If a spectrum with a spectral resolution of 8 cm-1 is post zerofilled with an

additional zerofilling factor of 2, the digital resolution after the interpolation is
4 cm-1.
Example 2
If a spectrum with a spectral resolution of 8 cm-1 is post zerofilled with an

additional zerofilling factor of 8, the digital resolution after the interpolation is
1 cm-1.
Note in both cases, however, that the spectral resolution is still 8 cm-1. To avoid
artifacts allow at least 50 more data points on each side of the desired interval.
This region must also contain meaningful spectral information.
In the example given in Figure 143 a post zero filling factor of 4 was used.

Manipulate
before Zerofilling
Figure 143: Digital Resolution before and after Post Zerofilling
8.23 Fourier Self Deconvolution
This option performs a Fourier Self Deconvolution (FSD) of a spectrum. The

aim of this operation is to enhance the apparent resolution of a spectrum or to
decrease the width of all lines contributing to the spectral range under investiga-
tion. This aids in resolving a spectral range comprising overlapping broad lines
into narrower lines. Using FSD allows you to narrow down the line width of
broad envelopes in order to improve a separation of peaks and shoulders.
This function is only suited for envelopes much broader than the spectral
resolution.
The type of the line-broadening function (LBF) may be either Lorentzian or

Gaussian. The appropriate type depends on the nature of the line broadening
mechanism. In case of doubt it is recommended to start with a Lorentzian shape.
After you selected a file and frequency range, specify a deconvolution factor
and a suppression factor for the noise, or alternatively, a factor for the band
width and the resolution enhancement. Start the function using the Deconvolute
button.

Fourier Self Deconvolution
Figure 144: Fourier Self-Deconvolution
Theory:
FSD assumes that the experimental spectrum consists of well resolved, narrow
peaks which have been convoluted with the same sort of LBF. If the shape and
width of this LBF are known, its effect can be mathematically removed from the
spectrum. This is done in interferogram space where removal of the LBF simply
corresponds to multiplication by a deconvolution function being the inverse of
the Fourier Transformation of the LBF.
The deconvolution corresponds to a multiplication of the interferogram I(x)

with the deconvolution function, exp(a*x) for Lorentzian shapes and
exp(a*x*x) in the case of Gaussians. The deconvolution factor is the maximum
value of this function at the end of the x-interval used.
The amplification of the interferogram by the deconvolution also amplifies the

noise. Especially at the wings of the interferogram the Signal-to-Noise ratio
becomes small. To reduce the noise, an apodization with a Blackman-Harris
function is always performed at the same time such that the interferogram is
multiplied with the product of an ascending deconvolution function and a
descending apodization function. The product of both functions is 1.0 at the
zero path difference point and zero at the end of the interval. It exhibits a maxi-
mum between these boundaries. Its maximum value determines the maximum
net amplification of the interferogram.
A deconvolution factor of 100, 1000 and 5000 corresponds to a maximum net

amplification of 3.4, 12.8, and 40 for Lorentzians and 1.06, 3.2 and 16 for Gaus-
sians, respectively. For Lorentzians it is recommended to try deconvolution fac-

Manipulate
tors on the order 50, 100, 1000, 5000 and to stop, if over-deconvolution occurs
(resultant spectrum shows artificial oscillations).
The noise reduction factor should range from 0.0 to 1.0. It is the fraction of the
interferogram to which the combination of deconvolution and apodization is
applied. A value of 1.0 corresponds to the full interferogram. It is recommend to
start with a value of 0.5 (half of the interferogram). If the spectrum has been cal-
culated using a zero filling factor > 2, then a start value of 1 / (zerofilling factor)
is recommended.
Only spectral ranges with signals of comparable line width should be selected.
Broad signals cannot be deconvoluted if there are sharp signals in the same
range. At the boundaries of the selected range the intensities should be close to
zero. If this is not the case, the spectrum should be baseline corrected prior to
deconvolution.
Figure 145 shows the spectrum ABBOE05.0 before and after a deconvolution,
which has been performed using the parameters shown in Figure 144. The
intensity at the peak maximum position usually is higher than compared to the
original spectrum. However, the peak ratios are not changed.
Deconvoluted Spectrum
Original Spectrum
Figure 145: Original and Deconvoluted Spectrum
8.24 Symmetric Fourier Transformation
Symmetric Fourier Transformation is used if a phase correction is not neces-

sary, because the data contains one half of a symmetric or antisymmetric inter-
ferogram. This may occur for example, if the interferogram was generated by an
inverse FT.

Kramers-Kronig Transformation (KKT)
Again, it is advised that if the interferogram is perfectly symmetric or perfectly

antisymmetric you should select the symmetric transformation. Define the data
range used for the transformation on the Frequency Range tab and start the
transformation. The result is a single channel spectrum. In case of an antisym-
metric transformation only the real part of the single channel spectrum will be
saved.
8.25 Kramers-Kronig Transformation (KKT)
This function can be used to extract additional information from a reflectance

spectrum such as the complex refractive index, the complex dielectric constant
and the phase change upon reflection. Furthermore, a reflectance spectrum can
be transformed into an absorbance spectrum. The following requirements must
be met:
• the sample must be homogeneous and pure (no blends, mixtures, lay-
ered systems or powders).
• the beam must be measured in specular (not diffuse!) reflection at a
small angle (e.g. 10 deg) at nearly normal incidence.
• the sample must be thick enough to ensure that no light is reflected
from the back surface. Ensure that no multiple reflections and inter-
ferences occur. If the sample is not thick enough to absorb all radia-
tion, roughen the backside to prevent reflection.
• the spectral cutoff must fall in a moderately flat and unstructured
region
Unlike an absorbance spectrum measured in transmittance, the calculated spec-

trum only describes the intensity loss within the sample due to absorption. It
does not account for the reflection losses at both boundaries of the sample layer.
For better comparison with experimental absorbance spectra, the reflection
losses can be taken into account by adding the term -2lg(1-[input - reflectance
spectrum] to the computed KKT-absorbance using the OPUS spectrum calcula-
tor.

Manipulate
Figure 146: Kramers-Kronig Transformation
On the first tab, the spectra to be processed are selected and the desired target
function is specified. Either the Refractive Index (Complex), the Dielectric
Function (Complex), the Absorbance spectrum or the Phase spectrum can be
computed. In the first two cases the target file will contain two data blocks: the
real and the imaginary parts of the function (as indicated by “R” or “I” in the
file symbol).
Theory:
The real and imaginary parts of complex physical quantities describing the
interaction of radiation with a sample (e.g. the complex refractive index
n = n + ik , the dielectric constant ε = ε′ + iε″ and the logarithm of the
amplitude-reflectivity ln ( re iφ ) = ln ( r ) + iφ ) are not independent from one
another due to the causality principle. They can be calculated from each other
by the Kramers-Kronig Transformation. OPUS uses this by first calculating the
phase rotation angle φ ( ν ) (a function of the wave number ν) of an optically
thick sample from the measured reflectance spectrum R ( ν ) = r 2 ( ν ) with the
KKT relation. Then the reflectivity of the air/sample interface is calculated from
r ( ν ) and φ ( ν ) using the Fresnel equation:
iφ ( ν )
Γ ( ν )e = [n(ν) – 1] ⁄ [n(ν) + 1]
The real and the imaginary parts of the refractive index are calculated as
1⁄2
n ( ν ) = [ 1 – R ( ν ) ] ⁄ [ 1 + R ( ν ) – 2R ( ν ) cos ( φ ( ν ) ) ]
κ ( ν ) = 2R 1 ⁄ 2 ( ν ) sin ( φ ( ν ) ) ⁄ [ 1 + R ( ν ) – 2R 1 ⁄ 2 ( ν ) cos ( φ ( ν ) ) ]

Extrapolation
If desired, the dielectric function is calculated:
ε′ = n 2 – κ 2
ε″ = 2nκ
With the imaginary part of the refractive index, the so called absorption index
κ ( ν ) , the absorptivity A ( ν ) of a layer having a thickness d can be calculated
as:
A ( ν ) = log ( e )2πνdκ ( ν )
In principle all important optical properties can be determined from of a single

reflectance spectrum R ( ν ) .
A separate description on using the KKT and some examples are available upon
request.
8.26 Extrapolation
You can extrapolate reflectance spectra to 0 cm-1 or to a wave number limit that
the user can set. For the extrapolation to 0 cm-1 we distinguish between insula-
tors and semiconductors. OPUS interprets the sample as a semiconductor if the
input for R (0 cm-1) is 1.
Select the spectrum and the frequency range as usual. Specify a limit for R at 0
cm-1 and at infinity. Start the calculation with the Extrapolate button.
Figure 147: Extrapolation

Manipulate
Extrapolation to 0 cm-1
The parameters R0 and i1 are used for the extrapolation to 0 cm-1. R0 can be any
value between 0 and 1. i1 represents the inner limit of the wave number interval
used to determine the fit function for the extrapolation. The beginning of the
original spectrum will be automatically chosen as the second limit i2. If for i1 a
wave number smaller than the lowest wave number of the original spectrum
was entered, i1 will be set to include two data points to fit the function.
R
new Orginal Spectrum new
1
R0
R∞
0
0 i1 i2 νend ν[cm-1]
Figure 148: Parameters Used for Extrapolation
Theory for Extrapolating n to 0 cm-1 in the Case of Semi-

conductors
OPUS uses the following approximation:
a 42
Φ4 = 1 – a4 ν + ----- ν + a 5 ν 1.5
2
Because R ( s ) = Φ ( s ) is already determined (“s” being the first wave number

of the spectrum), coefficient a5 can be eliminated
a 42
R ( s ) = 1 – a 4 s + ----- s + a 5 ν 1.5
2
a2
R ( s ) – 1 + a 4 s – ----4- s
2-
a 5 = --------------------------------------------------
s 1.5
We thus obtain:
a 42 a 42 ν 1.5
Φ 4 = 1 – a 4 ν + ----- ν +  R ( s ) – 1 + a 4 s – ----- s  ---
2  2   s
Now a4 should be chosen in a way that the sum of the squares of the error in the
region of overlap becomes a minimum.

Extrapolation
Theory for Extrapolating n to 0 cm-1 in the Case of Insula-

tors
Φ1 = R ( 0 ) + a1 ν 2 + a2 ν 4
Because R ( s ) = Φ ( s ) is already determined (“s” being the first wave number

of the spectrum), the coefficient a2 can be eliminated:
R ( s ) = R ( 0 ) + a1 s2 + a2 s4
R ( s ) – R ( 0 ) – a1 s2
a 2 = ---------------------------------------------
s4
We thus obtain:
ν 4
Φ 1 = R ( 0 ) + a 1 ν 2 + ( R ( s ) – R ( 0 ) – a 1 s 2 )  ---
 s
Now a1 should be chosen in a way that the sum of the squares of the error in the
region of overlap becomes a minimum.
Extrapolation to infinity
The extrapolation to infinity uses the parameters R∞, i1 and νend. R∞ and i2 are
equivalent to R0 and i1 in the above section, respectively. νend represents the
wave number up to which the extrapolation should be performed.
Approximation for Extrapolating n to Infinity

a a
Φ 3 = R ( ∞ ) + ----1- + ----2-
ν2 ν4
Because R ( s ) = Φ ( s ) is already determined (“t” being the last wave number

of the spectrum), coefficient a2 can be eliminated:
a a
R ( t ) = R ( ∞ ) + ----1- + ----2-
t2 t4
a
a 2 =  R ( t ) – R ( ∞ ) – ----1- t 4
t2
We obtain:

Manipulate
a t 4
Φ 3 = R ( ∞ ) + a 1 ν 2 +  R ( t ) – R ( ∞ ) – ----1-  ---
 t 2   ν
8.27 Abscissa Conversion
This function changes the x-axis units of a spectrum. Wave numbers are con-
verted to micrometer and nanometer or vice versa. You can load the spectrum
by dragging it from the browser into the window. The conversion direction can
be selected in the box on the right side of the dialog.
Figure 149: Abscissa Conversion – Conversion Direction
The frequency range can either be defined by the user or can be taken from the
original spectrum.

Abscissa Conversion
Figure 150: Abscissa Conversion – Frequency Range
The type of interpolation is determined by the “Max. Compression Factor”

(MCF) or the number of data points in the result of the conversion. If fixed fre-
quency limits were chosen you can define the number of data points after the
conversion was performed. Using the frequency limits of each file, the interpo-
lation depends on the MCF.
Figure 151: Abscissa Conversion – Scaling
Using Preserve Integrals has the effect of multiplying the y-values with a fre-
quency- or wavelength-dependent factor (proportional to 1/x2), so that integrat-

Manipulate
ing the original spectrum and the new spectrum within the same limits yields
the same sum.
The user can also scale the intensities of the converted spectrum. When you
select Preserve y-Values, the intensities will be taken from the original spec-
trum. The spectrum generally looks the same (with a significantly changed y-
axis).
Theory:
The wave number ↔ micron conversion is calculated using the following for-
mula:
wavelength (micron) x wave number (cm-1) = 10000.
A digitally recorded spectrum consists of equidistant data points, e.g. two data
points per wave number. However, after the conversion to wavelengths the data
points are no longer equidistant because of the hyperbolic conversion function.
Since OPUS saves spectra as a set of equidistant data points only, an interpola-
tion must be performed after the abscissa conversion.
Wave number [cm-1] Wavelength [µm] Difference [µm]
400 25.00
1.19
420 23.81
1.08
440 22.73
0.99
460 21.74
0.91
480 20.83
0.83
500 20.00
The interpolation type is determined by the maximum compression factor

(MCF) or the number of resulting data points. The minimum number of data
points for the wavelength spectrum is the number of data points found in the
input (cm-1) spectrum. The MCF defines the conversion properties in the high
frequency end of the wave number spectrum which is converted to the low
wavelength end of the micron spectrum.
If a factor of 5 is chosen, five frequency intervals (data point spacings) are con-
verted to one wavelength interval and spectral information is lost. The ratio gets
better when lower wave numbers (higher wavelengths) are observed. The MCF
can be varied between 0.5 and 50 but the new spectrum never has fewer data
points than the original spectrum. The number of data points does not change
for a factor of 20 or larger.

Abscissa Conversion
Using a small MCF the number of data points of the new spectrum may become
rather large. This depends on the start and end frequency and the frequency
interval of the original spectrum. By back-transformation of the micron spec-
trum and comparison with the original spectrum a reasonable factor can be cho-
sen.
In Figure 152 the upper-left graph shows the original data scaled in wavenum-
bers. The spectrum on the right side has been converted to wave numbers, with
the intensities remaining unchanged. The lower-left spectrum has been con-
verted and the integrals of the intensities were preserved. The last graph shows a
conversion and re-conversion of the original data (B) to wave numbers, using a
MCF of one (A) and of 15 (C). The number of data points in (A) is about ten
times higher than in (C), and is a better representation of the original data.
Figure 152: Original Data and Converted Spectra after Abscissa Conversion

Manipulate
8.28 Averaging
The Averaging function generates an average spectrum from a set of original

spectra of the same type.
Figure 153: Averaging
Select the spectra either by dragging the from the browser into the selection
window (Select by Symbol) or by specifying their names (Select by Name). In
the latter case you also have to specify the path and the data block of the files.
The calculated average spectrum will only be saved to disk if you check the
Update A. Spectrum box; an additional field will be displayed in which you
have to enter the name of the file to be saved. If a file with this name already
exists it will be automatically included in the average set and replaced by the
result file.
If the checkbox Weighting with No of Scans is checked the averaging is carried

out by weighting the selected data files. In this case each spectrum is weighted
proportional to the number of scans measured for each file.
If you select Create/Update Std.-Dev. Spectrum a second spectrum is generated

in addition to the averaged spectrum, whose intensity is given by the relative
standard deviation of the averaged spectra.
You can also create an average report, which contains a comparison of the orig-
inal set of spectra with the average spectrum. In this report the distances of the

Merging Spectra Ranges
averaged spectrum to the original spectra are listed. These distances are given in
multiples of the standard deviation to make the detection of outliers easier. You
will also find listed in the report the method that was used for averaging the
spectra and the frequency region of the calculation. Select the method by click-
ing on the Report Method button. The methods are saved in files with the exten-
sion .faa
Theory:
Upon averaging the arithmetic mean intensity y of the n input spectra is calcu-
lated:
n
∑
i=1
yi
y = --------------------
n
For n averaged spectra, the standard deviation σ is:
n 2
∑
i=1
( yi – y )
σ = ------------------------------------
n–1
Standard deviation spectra calculated with and without weighting the number of
scans appear different even in cases where the number of scans is the same for
all spectra. This is due to the equation denominator (n – 1 vs. n) where n is the
number of scans, not the number of averaged spectra. The result is therefore dif-
ferent by a constant factor. For a large number of input spectra, this factor
approaches 1.
8.29 Merging Spectra Ranges
Spectra of the same type (e.g. absorbance spectra) can be linked together to
form a new spectrum. Any gap in the frequency region is filled with a straight
line.
If two spectra to be merged overlap, linear weighting is performed to avoid a

step. If the total x-range of one of the spectra to be merged covers that of
another spectrum (i.e. one spectrum is superfluous), OPUS gives a warning
message and stops the function. The parameter set of the new spectrum is cop-
ied from the first spectrum to be merged.
To merge spectra, drag them on the Select Files window and click on the Merge
button.

Manipulate
Figure 154: Merging Spectra Ranges
Result of Merging Spectra Range
Two Separate Spectra
Figure 155: Original and Merged Spectra

Curve Fit
9 Evaluate
The Evaluate menu is primarily intended for calculating results from existing
spectra. This could be a quantitative data analysis, peak identification or a
library search. These function do not alter the spectrum files.
Figure 156: Evaluate Menu
9.1 Curve Fit
Curve Fit is a function used for the calculation of single components ins a sys-
tem of overlapping bands. A model consisting of an estimated number of bands
and a baseline should be generated before the fitting calculation is started.
The model can be setup interactively on the display and is optimized during the
calculation. Since the result of thee calculation is highly dependant on the
model chosen, care must be taken that the model is reasonable from the chemi-
cal point of view.

Evaluate
Setup Model
On selecting the function from the Measurement menu, a dialog box appears for
the section of the spectrum and the frequency range.
Figure 157: Curve Fit - Select Spectrum
On the first tab of the dialog, the spectrum to be fitted is selected by dragging it
from the browser window into the File to Fit box. Note that the spectrum needs
to be of absorbance type and baseline corrected.
If Save Single peaks Too is checked, every fitted peak will be stored as a sepa-
rate file.
In the second tab of the dialog box, you can select the frequency range of the
spectrum you want to fit. Interactive leads you to a new window where you can
chose the area to fit interactively. Get Display Limits takes the limits from the
respective display window. When ticking Use File Limits, the original fre-
quency range of the file is taken. The previous two options are then blanked
out.
Once a suitable model has been found (see next paragraphs), it can be applied to
other spectra of the same kind, there is no need to setup a new model for each
spectrum. The spectra to be analyzed must be selected into the top window.
The Fit Report block ( ) of the already fitted spectrum is then dragged into
the second box. Clicking onto Fit starts the Curve Fitting of all spectra with the
selected method.

Curve Fit
Figure 158: Curve Fit - Frequency Range
To perform a curve fit, a fit method must be created first. By clicking onto Start
Interactive Mode, the spectrum you selected will be opened in the curve fit
setup window (see Fig. 158).
In the upper window, the spectrum to be fitted is displayed, whereas in the bot-
tom window the difference between the original spectrum and the fitted spec-
trum is shown. As there was no fitting carried out at this point, both windows
show the same spectrum.
You can create a curve fit model by moving the cursor into the top window. The
mouse pointer will change from an arrow to an ADD symbol ( ). By click-
ing onto the peak, a curve will appear close to the selected peak. Each left click
will generate a new curve. The intensity of the curve corresponds to the cursor
position. The generated curves will appear in red.

Evaluate
Figure 159: Curve Fit Window before Fit
When the cursor is positioned close to the top of the peak, the MOVE symbol
( ) is displayed. You can now move the curve by clicking and dragging it to
the desired position.
To change the width of the peak, position the cursor slightly below the top of
the curve. The WIDTH symbol ( ) will appear. By clicking and dragging to
the left, the curve will become wider, whereas dragging to the right makes the
curve narrower.

Curve Fit
Figure 160: Curve Fit Window after Fit
Peak Parameters
In the bottom half of the window, various parameters can be edited. Position,
Intensity and Width can here be manipulated more precisely than with the cur-
sor. To change the values of a curve, it must be selected first by clicking onto
the respective field. Than the values can be directly typed in or changed with
the respective arrow key above the field.

Evaluate
Peak Shape
Several different options exist for the peak shape. The default setting is Lorentz,
i.e. a pure Lorentzian curve. A single click on the upper arrow key switches
immediately to a pure Gaussian function. The next click on the same arrow sets
the peak to Baseline. If, beginning again with the Lorentz type, the down arrow
is clicked on instead, the peak shape changes to 100%Lorentz + Gauss. In
principle the peak shape simulated is also a pure Lorentzian function but it rep-
resents the special case of a mixture of Lorentzian and Gaussian functions.
Repeated clicking, on the down arrow manually decreases the Lorentz function
percentage. This type of manipulation is typically left to be performed by
OPUS.
Baseline
In some cases it may be necessary to use a Baseline in addition to the peaks. A
baseline is always a straight line defined by a reference point and a slope. The
baseline can be defined by the operator or calculated by OPUS. The parameter
Width is replaced by Slope in the peak list. Baseline parameters can be set inter-
actively with the mouse or directly in the peak table.
The parameters of the baseline are automatically modified only if the Leven-
berg-Marquardt algorithm is used. If the Local Least Squares algorithm is
selected, the parameters are set manually.
Peak List
Each peak is shown in one line of the peak list including all peak parameters.
The lines with non-selected peaks are green and the currently selected peak is
marked in violet. The peaks in the list are always sorted by peak position. Algo-
rithm
Two different algorithms are available for the optimization of the model:
• Levenberg-Marquardt
• Local Least Squares
The algorithm can be selected before starting the calculation but can also be
changed during the calculation. The algorithm principles are described below.
Status Line
The status line is activated after starting the calculation. It shows the iteration
time and the error of the fit.
Example: 12 sec: Residual RMS error 0.009109

Curve Fit
The smaller the error value the smaller the deviation between measured and cal-
culated curve.
Message: * Bad Fitting Model! *
Sometimes an additional message *Bad Fitting Model!* is displayed in the sta-

tus line. This message is displayed if the program was not able to fit one or more
peaks. These peaks are found at the left or right end of the frequency range and
usually have very small intensities. These bands needs to be deleted before the
calculation is continued. To delete a band, click on its band number (left row) to
select the band and press Delete on your keyboard.
Max Iter. Time (sec)

The maximum iteration time for Auto Fit in seconds is specified in this field.
Auto Fit
The Auto Fit button is used to start the calculation. After clicking on this button
the calculation begins and the button text changes to Stop. During the iteration
the newly calculated peaks are shown on the display in real time. The calcula-
tion can be interrupted at any time by clicking on the button. To restart, click the
button again.
Autoscale
At any time, the standard display functions can be used to zoom, expand or roll
the contents of the display. To return to the original frequency and intensity lim-
its click on the Autoscale button.
Save Report
Select the Save Report button to save the current report. The resulting sum-
spectrum is stored as a temporary work file. This fit report can be used for the
curve fit of new spectra.
Save Peaks and Reps

In addition to the previously described functions for the Safe Report button, the
fit report is added to the original spectrum.

Evaluate
Theoretical Background
Two different algorithms are used for the curve fit:
• Levenberg-Marquardt
• Local Least Squares
Both algorithms are based on the least squares method. The difference between
the original and the calculated curve are kept as small as possible. The fitting
model is described by:
Y G = y ( x ;S )
YG Measured data
y Model
x Frequency
S Set of curve parameters
Levenberg-Marquardt Algorithm
The quadratic equation for the deviation between measured and calculated
curve is:
N
2 2
χ (S) = ∑i = 1 [ Y G – y ( x ;S ) ]
χ2 Quadratic deviation
N Number of points
The function is minimized by iteration. The gradient of the function χ2 is calcu-

lated for the current set of peak parameters. The gradient is then used to deter-
mine a new set of parameters S.
Some additional restrictions have also been implemented to make the calcula-
tion more effective:
• All peaks must lie within the specified frequency range.
• The width of a peak must not be greater than the specified frequency
range.
• Peak intensities must be positive.
• The contribution of Lorentz- and Gauss functions for mixtures must
lie within the range 0% to 100%.
• The sum of both parts must always be 100%.

Integration
Local Least Squares Algorithm

The Local Least Squares algorithm performs an independent fit for each indi-
vidual peak. The calculation is thereby restricted to the range around the peak
maximum. This dramatically reduces the amount of data required for the calcu-
lation, enhancing the speed compared to the Levenberg-Marquardt method.
Some loss of precision vs. the Levenberg-Marquardt method occurs.
The Local Least Squares algorithm has some conditions:

• The parameters for the baseline are taken from the model, not calcu-
lated.
• The peak parameters are always variable, none of them can be fixed.
The given model can be looked at as an area in a n-dimensional space with n

being the total number of peak parameters. In most cases this area has one abso-
lute minimum and several local minima. The quality of the calculation depends
on the quality of the selected model, i.e. does the calculation find the absolute
minimum or does it orbit in the vicinity of the local minima. The latter case can
be detected by a relatively large error and an visually obvious poor fit. In case of
a poor fit, start again with a new optimized model.
Criteria for the selection of an algorithm

The Levenberg-Marquardt algorithm in most cases gives a better fit compared
to the Local Least Squares algorithm, but needs significantly more calculation
time. If the number of points in the selected region and the number of peaks in
the model is small the Levenberg-Marquardt algorithm can be used immedi-
ately.
If the amount of data is large or many peaks need to be fitted, start with the
Local Least Squares algorithm which converges very quickly. As soon as the
variation of the error becomes small, switch to the Levenberg-Marquardt algo-
rithm for the final fit.
9.2 Integration
This function is used to carry out the integration of peaks as well as the calcula-
tion of peak heights. Seventeen integration types are offered.

Evaluate
Figure 162: Integration
The integration method must be defined by the user. The method defines both
the frequency ranges and the integration. Integration methods can be stored sep-
arately and loaded at any time. The last integration method used becomes the
default method until another method is loaded or a new method is created.
The currently loaded integration method is shown. If no integration method is

available, this text reads “No Integration Method loaded”. In this case an exist-
ing method must be loaded or a new method must be created.
Click on the Load Method button: The Load Integration Method dialog box
appears. Choose the desired directory path and integration method. Load the
method by clicking on the Load button.
When you create a new integration method, you can specify an integration
method for each peak of interest.
Performing the integration generates an integration report. It is represented in

the Browser by an data block icon. The report contains, in addition to the
numerical results of the integration, the method used and the frequency limits.
Figure 163: Integration Report

Integration
The integration report in Figure 163 shows the results of integrating two bands
(peak 1 and peak 2) using different integration methods. The displayed result
are the peak areas, other methods also give the peak intensities.
If the same spectrum is integrated a second time, you can choose between over-
writing the first integration report, merging both reports, or appending the new
report into the old one. The default setting will overwrite the report.
Figure 164: Integration – Report
• Overwrite – replaces the old report (default setting)

• Merge – adds the results to an existing report
• Append – generates a new report and adds it to the existing file
appended report
Figure 165: Appending a New Integration Report to an Existing One
Setting up an Integration Method
When creating an integration method you specify the frequencies for one or
more regions that are to be integrated.

Evaluate
(e)
(a)
(f)
(b) (g)
(h)
(c)
(i)
(j)
(d)
Figure 166: Integration Method Setup
a) Left and right limit for the integration.

b) One to four points used to determine the baseline.
c) Total number of frequency ranges.
d) Integration method used for the current region.
e) Number of the integration region currently displayed.
f) Forward and backward keys to switch between integration regions.
g) Clears the current region.
h) Input line for the name of the peak to be integrated.
i) Clears all regions of the loaded integration method. Should be used before creat-
ing a new integration method.
j) Loads a method for editing.
Note: Before you exit this dialog make sure you save your work. If you don’t
save your changes they will be discarded when you exit the dialog.

Integration
A) The integration will be performed between the frequency limits and the
peak envelope, using zero as the baseline.
B) The integration will be performed using as a baseline a straight line that

connects the frequency limits and the peak envelope.
C) Same as in B, but two separate data points will be used to define the base-
line.
D) Same as in B, but a straight line running through an additional point will be

used as baseline.
E) Same as in B, but the two points defining the baseline are averaged from
the first and the second, the third and the fourth point, respectively. The
average values together with the second and third point define the baseline.
Useful for “noisy” spectra.
F) Same as in B, but the baseline will be defined by a least square fit of a
parabola to the data points between the first and the second, and between
the third and the fourth baseline point.
G) Looks for the highest intensity in the frequency range. The baseline in this
region is then defined by the local minima.
H) Integrates from the maximum to the left minimum.
I) Integrates from the maximum to the right frequency minimum.
J) Highest absolute intensity of the peak.
K) Peak intensity relative to the local baseline.
L) Same as in C, peak intensity relative to the baseline.
M) Same as in D, peak intensity relative to the baseline.
N) Same as in F, peak intensity relative to the baseline.
O) Minimum between the frequency limits.
P) Intensity at the specified frequency.
Q) Same as in E, peak intensity relative to the baseline.
R) Peak intensity at a given frequency.
Figure 167: Integration Modes

Evaluate
9.3 Quant 1
Quant 1 is the software algorithm used to determine component concentration

values for unknown samples. To quantify the components of a multicomponent
sample, calibration measurements are required.
Quant 1 is only suited for spectra with well separated peaks. In case of peak
overlap the use of Quant 2 is recommended.
9.3.1 Setup Calibration

Several samples are necessary for calibration. These calibration samples should
contain each component of interest in various concentrations. Furthermore, the
concentrations have to be known, i.e. were determined by a different analytical
method. Using these calibration samples their spectra can be correlated with the
compound concentration.
Each component is assigned to exactly one peak in the spectrum; there are 17
different possibilities (different baselines, intensity or area) to evaluate a peak.
Finally, a calibration function (linear, quadratic or polynomial) is fitted to the
data obtained from the calibration samples, and this function is then used to
determine the concentrations of the unknown sample.
IR spectra are usually depicted as absorption spectra. Ideally, for weakly

absorbing compounds, a linear correlation between the concentration and the
absorption is to be expected (Beer’s law).
A wizard will guide you through the setup of a Quant 1 calibration. Each step
will be performed on a separate tab of the dialog. Using the arrows you can flip
through the pages.
On the first tab a short overview of the necessary steps is given. You can also
load and edit an existing method; this can also be a method created with OPUS-
OS/2. In the following we will generate a new method:

Quant 1
Figure 168: Setup Quant 1
Switch to the next tab. Here you can enter the name of the components and their
units. Start by clicking on Add Component.

Evaluate
(a) (b) (c) (d) (e)
Figure 169: Define Components
The default name of the first component and the unit “mg” appears in the boxes
(a) and (b). If you like, choose a name representative of the compounds you use
and save it using button (e). To include additional compounds use Add Compo-
nent (d); list (c) displays all components and weights. To remove a component,
select it with the mouse and press the delete key on your keyboard.

Quant 1
Figure 170: Component List
On the next tab you load the calibration spectra and enter the value of each com-
ponent for each sample of the calibration set. Using the Add Spectra button you
can include spectra in the list. Navigate to the directory holding the spectra by
clicking on Change Path. If you want to exclude a spectrum do so by selecting
the spectrum and press Remove Selected Spectra. You can also print this table
for your records.

Evaluate
Figure 171: Component List – Component Value Input
Finally, you need to pick a peak which is significant for each sample. Click on
Define Integration Method and choose an appropriate method as well as the fre-
quency limits as described in the chapter „Integration” on page 173.
In addition, you have the possibility to define a reference peak by placing a

mark in the Use Reference Peak checkbox. Select an integration method and
frequency region for this peak as you would for any other peak. Be sure to indi-
cate Reference Peak in the drop-down list. This reference peak will be used to
normalize the spectrum.
Figure 172: Defining the Integration Method

Quant 1
Figure 173: Setup Integration Method
As the final step you must define the type of calibration function you would like
to fit to your calibration set. While a linear function is suitable for samples
which obey Beer’s law, deviations can be taken into account by choosing a qua-
dratic or cubic function.

Evaluate
Figure 174: Choose Calibration a Method
After you have set up your Quant 1 method you will be asked to save the
method to disk. Usually, Quant methods will be saved in the “Quant” subdirec-
tory of the OPUS folder. Then the computation of the calibration function starts.
Depending on the number of calibration spectra, this may take up to a few sec-
onds or longer.
Click on Next to display the results of the calibration. Each component has its
own tab. The first column lists the file names of the calibration set. The true
value (i.e. the known amount of the substance) and the value calculated by the
fit are given in the next two columns. The difference between these values, the
error of the calculated value and the peak size “X” calculated from the spectra
are also shown.

Quant 1
Figure 175: Calibration Results
You can switch between the result pages for each component using the arrow
button. Toggle between the tabular view and a report view of the results by
selecting the Calibration Report checkbox. The report view will give you a
printable version of the report. Clicking on Next will get a graph of the calibra-
tion result. The graph allows one to easily recognize data with poor correlations
(for example incorrect values caused by typographical errors during data entry).

Evaluate
Figure 176: Graphic Display of Calibration Results – Fit vs. True
Below the graphics, The method file, the correlation coefficient and the calibra-
tion equation are stated.
Using the pull-down menu at the bottom of the graph you can switch between
different representations of the calibration result: “Fit vs True” displays the val-
ues obtained by the fit against the known (true) values of the component. Other
options are “Difference vs. True” or “True vs. X”.

Quant 1
Figure 177: Graphic Display of Calibration Results – Difference vs. True

Evaluate
Figure 178: Graphic Display of Calibration Results – True vs X
You can print the results, the figures as well as the data tables, using the Print
button. A report of the results including the calibration equation is stored
together with the method file. Exit the program by clicking on Finish.
9.3.2 Quant 1 Analysis

After you have created a calibration set you can now start to analyze your sam-
ples. Keep in mind that the concentration of the samples should fall within the
concentration interval covered by the calibration set. Furthermore, the spectrum
of the unknown sample must be acquired using the same parameters as for the
spectra of the calibration set.

Quant 1
Figure 179: Quantitative Analysis
Select the spectra you wish to analyze and load the appropriate Quant 1 method.
If a method had been created or loaded before, it will automatically be available
for the analysis.
Click on Analyze to start the analysis. The result will be saved in a Quant 1 data
block together with the analyzed spectrum and the spectra will be marked as
modified in the browser.
Figure 180: Quant Info Block
Like every other report, you can read Quant reports by opening a report win-
dow. Open the header of the report by right-clicking on the report window. The
header contains the name of the Quant method used for the analysis and the date
the method was created. The report lists the component names, their predicted
concentration together with their units, the correlation coefficient sigma and the
results of the peak integration.

Evaluate
Figure 181: Quant 1 Report
You can apply more than one Quant method to analyze a spectrum; the resulting
reports are saved in the same report data block. They appear as entries in the
tree of the report window. Switch between reports by clicking on the report
name of the tree.
Figure 182: Quant 1 Report Header
Theory:
The functions used for the calibration will be saved in the calibration record as
Y = f(X); where the Y are the values obtained by the fit and X is the peak size
obtained from the spectra. Sigma is a parameter representing the difference
between predicted and true value. Keep in mind that the “true” values are also
prone to statistical errors, depending on how carefully they have been deter-
mined. An indication for the quality of the calibration is the correlation coeffi-
cient r:
∑ ( ( Zi – Zm ) ( Yi – Ym ) )
r = --------------------------------------------------------------------
∑ ( Zi – Zm ) 2 ∑ ( Yi – Ym ) 2
Here, Z stands for the true concentrations of the components, while m is the
respective average value. The correlation coefficient should be close to 1.0.
The error in analyzing samples of unknown concentration can be estimated by

σ. There is an approximately 68% probability that the concentration of the
unknown sample falls within an interval of the predicted value plus or minus σ:
1 -
M – f∑ i
σ = ----------- ( Z – Yi ) 2
M: number of calibration samples

f: degree of freedom (linear 2, quadratic 3, cubic 4)
Z: true concentration
Y: predicted concentration

Signal-to-Noise Ratio
9.4 Signal-to-Noise Ratio
This function calculates the Signal-to-Noise ratio (SNR) of a spectrum over a

given spectral range. The results may be stored with the spectrum.
Two S/N values are calculated: RMS (Root Mean Square) and PP (Peak to
Peak). In both cases a function is fitted to the spectrum in the region of interest.
This function is either a straight line or (optionally) a quadratic parabola. This
curve defines the (nominal) signal. RMS is calculated as the root of the mean
square of deviations (i.e., the standard deviation). PP noise is the peak to peak
excursions (maximum - minimum) in the y-direction.
Some spectra types (e.g. Absorption, Emission) have base lines near zero. Spec-
ifying a Signal-to-Noise ratio makes no sense in these cases.
The (mean) nominal signal is divided by the newly calculated noise values and
yields the SNR. The result for the PP SNR is always smaller (“worse”) than that
for the RMS value.
Figure 183: Signal-To-Noise Ratio
You can choose the parabolic fit function by checking the Fit Parabola box,
otherwise a linear function is automatically fit to the data. Click on Show to dis-
play the results of the fit. If desired, you can save the fit in combination with the
spectrum.

Evaluate
Figure 184: Select a Frequency Range from the Pull-down Menu
The frequency range is entered on the second tab; in addition to manual input,
pre-defined spectral ranges are provided.
Figure 185: Signal To Noise Evaluation
Minimum and Maximum gives the extrema of the ordinate values over the eval-
uated range. To locate the results of a SNR calculation, open a new report win-
dow by right-clicking on the “Display” icon in the Browser. Drop the file of
interest into the report window and open the “Data Parameters AB” branch
(alternatively, right-click directly on the file name and choose Show Parame-
ters).

Peak Picking
Figure 186: Report Window Showing Data Parameters AB Branch
9.5 Peak Picking
The Peak Picking command helps you to identify peaks in your spectra. The
command offers high flexibility by allowing you to adjust and fine tune the
search parameters.
First, select the spectrum and the region of interest as usual. Define the Sensitiv-
ity. This is the most important parameter for the identification.
Figure 187: Peak Picking – File Selection

Evaluate
Now you can either choose the interactive mode or switch to the next tab to con-
tinue with the automatic mode. To switch to the interactive mode click on the
Start interactive mode button. According to the threshold value set on the slider
the number of identified peaks changes.
Figure 188: Peak Picking – Interactive Mode
Next select up the Y-limits tab. Depending on your data, i.e. whether low-inten-
sity peaks are crucial or not, you can specify the intensity range important to
your problem.

Peak Picking
(a)
(b)
Figure 189: Peak Picking – Y-Limits
Values entered at (a) and (b) reduce the hit number. (a) allows you to define the
peak intensity in relation to the surroundings of the peak and the baseline. Using
option (b), you can also specify the limits as absolute absorption values.
In the case of absorbance spectra usually the maxima are of interest, whereas for
transmittance or reflectance spectra the minima are the important features. This
can be accounted for by selecting the appropriate peak picking mode. The Auto-
matic mode uses the spectrum type information stored in the data block to deter-
mine if maxima or minima are picked.
In rare situations (e.g. for subtraction or photoacoustic spectra) it is necessary to

specify whether the algorithm should pick for minima (i.e. transmittance spec-
tra) or for maxima (i.e. absorbance spectra).

Evaluate
Figure 190: Peak Picking – Mode
By default OPUS determines the number of figures after the decimal used for
the wave number value from the spectral resolution. The user has the option of
defining this number in the user settings. If you use Peak Pick on a spectrum
that already has a peak list associated, you can choose between overwriting the
old list with the new one or to append the new list to the existing one.
To be independent of the baseline, the second derivative algorithm is typically

used, since the first derivative does not isolate peaks sufficiently well in case of
weak shoulders. The Savitzky-Golay algorithm is actually used to obtain the
derivative. Again, the number of smoothing points used can be adjusted to sup-
press the effect of noise. As a rule of thumb, one should not use a larger number
of smoothing points than the full width at half maximum of the smallest peak of
interest.
Theory:
The standard method is used for peaks with small or no overlap in spectra of
low or average spectral resolution (0.5 cm-1 or above).
The x-position is the x-value of the interpolated maximum or minimum, with

intensity being the y-value of this point. To determine the relative intensity an
internal local baseline between two lateral minima (or maxima) is drawn. The
relative intensity is then the y-axis distance between this baseline and the maxi-
mum (or minimum).

Peak Picking
Full Width at Half

Maximum
Relative Intensity
Local Baseline
Figure 191: Spectrum with Line width, Relative Intensity and Baseline Indicated
The lateral extremes are determined by going outwards from the x-position of
the line, until another line at least as strong is found (or the end of the spectrum
is reached). The lowest point in this interval is then used as a lateral minimum
(or maximum).
To find the line width, a line parallel to the local baseline is drawn which inter-
sects the middle of a vertical line connecting the maximum (or minimum) of the
band and the local baseline.
Peaks will be included in the peak pick table if their relative intensity falls
within the interval defined on the Y-Limits tab. This interval was normalized
such that the difference between maxima and minima corresponds to 100%.
The definition of the upper limit is optional and can be used to mask, for exam-
ple, large water bands.

Evaluate
Figure 192: Calculation with Baseline Reference
The peak search using the second derivative method is recommended for high
resolution spectra only.
2nd derivative
Figure 193: Absorption Spectrum and Second Derivative
The x-positions are the x-values of the minima (or maxima) of the smoothed,
second derivative spectrum. This is particularly useful for seriously overlapping
bands because in this case an extremity of the spectrum is frequently not shifted
with respect to the true band position. Weak shoulders can also be recognized
using the second derivative method.
In order to calculate the relative intensities and the width of the peak, the zero-
points and the minima of the second derivative are computed. These points are
significant for the peaks that make up the envelope:

Peak Picking
[ν-1, 0] (zero-point)
[ν0, I"0] (minimum)
[ν1, 0] (zero-point)
In Figures 194 and 195 two Lorentzian curves are superimposed. The zero-
points and the minima of both signals are almost identical (both for the deriva-
tives of the isolated signals as well as for their superposition). The maxima of
the overlapped signals are shifted and therefore misleading.
If a strong signal overlaps a weak signal, a maximum could be found where a

zero-point should be. If a maximum is found prior to a zero-point, during the
search for a minimum of the second derivative, the position of the maximum
has to be used instead. This points to the limitations of the method.
Apparent Peak Positions
True Peak Positions
Figure 194: Two Overlapping Signals
Apparent Peak Positions
True Peak Positions
Figure 195: A Weak Signal Superimposed on a Stronger Signal

Evaluate
To access the Peak Table, right-click on the Peak Pick report block and select
the Show Peak List command from the pop-up menu. A table created using the
standard method for low resolution spectra and relative intensities of higher
than 10% (accuracy to 4 decimal points) could look like the following:
Figure 196: Result of a Peak Search
9.6 Quick Identity Test
The Quick Identity Test offers a user friendly method to judge the similarity of
two spectra. This method requires a reference spectrum of the substance of
interest. The test determines the Euclidean distance between the test and refer-
ence spectrum.

Quick Identity Test
Figure 197: Quick Identity Test – Selected Files
Enter the reference spectrum in the field Principal File for Quick Identity Test,
and the files to be tested in the field Files for Quick Ident.
Figure 198: Quick Identity Test – Frequency Ranges

Evaluate
You can define several frequency regions on the second tab; only the data of the
regions indicated here will be compared. Or you can compare the frequency
range common to all spectra by checking the Use File Limits box. Switch
between regions with the arrow key. Delete a region by clicking on the Clear
button.
Select a two data preprocessing method, the derivative or the vector normaliza-
tion. A vector normalization causes the Euclidean distance to fall within an
interval of 0 and 2.
Figure 199: Quick Identity Test Report
A report block will be appended to every spectrum which was compared to the
reference spectrum. This “Report of Correlation Search” lists the spectrum
name and sample name (as taken from the spectrum parameter block), the num-
ber of the spectrum, the “Hit Quality” and the file name. The hit quality should
preferably be a small number, with zero being an absolute match.
In addition, a new file “QIDNT.0” will be created that summarizes the reports
of all test spectra. The report headers of this report are identical with the headers
of the respective test spectra reports. In these headers you find information
about the method applied to compare the spectra. The report is structured simi-
lar to an OPUS/IDENT report; IDENT is available as an additional package and
allows you to vary multiple parameters which can’t be changed in the Quick
Identity Test. An assessment of “identical” or “not identical” is not possible here
because no threshold information is available from an IDENT method or a stan-
dard deviation spectrum in the evaluation.

Conformity Test
The following information is of relevance when using the Quick Identity Test:
Method file: file name of the method used for the

test
Expected Reference: the principal file used.
Vector normalized spectra: indicates that vector normalization
was used.
X-Ranges: number of frequency ranges.
Order of Internal Derivation: gives the order of the derivative used.
Smoothing Points for Internal Derivation:gives the number of smoothing
points.
9.7 Conformity Test
The Conformity Test is a simple method to check the identity of a measured

spectrum against a single reference spectrum (instead against a library of refer-
ence spectra). Compared to the IDENT software package, the Conformity Test
function compares each spectrum data point by data point.
To carry out this test three spectra are required:

• a query spectrum to be tested
• a reference spectrum
• a standard deviation spectrum
The reference spectrum and the standard deviation spectrum must be calculated
from a previous set of measurements, using the Averaging function (see
chapter 8.23 for details).

Evaluate
Figure 200: Conformity Test – Selected Files
On the first tab of the dialog you specify the reference spectrum, the standard
deviation spectrum and the spectrum to be tested.
Figure 201: Conformity Test – Save Method

Conformity Test
Once you have set up a Conformity Test method you can save it to disk. These
method files have the extension .con and can be loaded from the second tab of
the Conformity Test dialog box.
Figure 202: Conformity Test – Parameters
You need only specify two parameters to perform the test: a frequency region
and the standard deviation factor (F, see below). Select the frequency region as
usual, either by manually entering the values in the table or interactively. Enter
the factor for the standard deviation in the SDev Fact for Conformity field and
start the algorithm by clicking the Conformity Test button.
The test result will be appended to the query spectrum file in form of a report
block. Figure 203 shows two reports, one with a negative result and one for a
query spectrum found identical to the average spectrum. In the first case the
largest deviation was found to be 3.057531 the standard deviation, which lies
well above the threshold of 2.

Evaluate
(a)
(b)
Figure 203: Conformity Test Report – Non-Identical (a) and Identical Spectra (b)
Theory:
The average spectrum serves as a reference while the standard deviation spec-
trum is used to define the allowable deviation from the reference spectrum. The
test spectrum Test(ν) is not allowed to deviate more than ± F ⋅ SDev ( ν ) from
the average spectrum Ref(ν). The following condition must be met:
Test ( ν ) – Ref ( ν ) < F ⋅ SDev ( ν )
Otherwise the spectrum is not considered identical with the reference.
9.8 Quality-Test
The quality assessment of spectra measured using the Quality-Test command is

an integral part of spectral analysis and should always be carried out before the
actual evaluation.
This test assesses the quality of spectra measured with regard to absorbance val-
ues, signal-to-noise ratio and intensity of the water vapor lines. Spectra that
exceed certain limit values should not be considered for analysis.
Select the Quality-Test command from the Evaluate menu. The following dia-
log box (see Fig. 204) opens:

Quality-Test
Figure 204: Quality Test - Select Files
The Select Files tab includes the spectrum to be tested. You can drag and drop
the file icon from the browser window into the File(s) for Quality-Test field.
Note that the spectrum to be evaluated needs to be an absorbance spectrum.
Click on the Quality-Test button to perform the test using the parameters of the
method currently loaded. To load or save a method, click on the Load/Save
Method tab of the Quality-Test dialog box.
Figure 205: Quality Test - Load/Save Method

Evaluate
The quality test results are stored in the Quality-Test Report data block ( )
which is added to the evaluated spectral file. Double click on the QTEST block
in the OPUS browser window to open the Quality-Test Report window. Figure
206 shows an example of a Quality-Test Report.
Figure 206: Quality Test Report
The first line of the report indicates the test result. A value of 1 means passed,
whereas 0 means failed. Do not use spectra that failed for further analysis. The
second line includes the file name of the test method used. The lower window
shows all parameters and their limits. These parameters can be defined if you
click on the Parameters tab.
Figure 207: Quality Test - Parameters

Quality-Test
Parameters
Some parameters and their limit values are explained in the following:
x-Range 1
In the range defined in the first column (2100 - 1600 cm-1) the maximum and
minimum absorbance values of the original spectrum ([AB] data block) are cal-
culated. The difference between these two values has to be higher than the one
indicated in the Delta y min entry field and lower than the limit defined in the
Delta y max entry field(0.345 to 1.245 absorbance units).
x-Range 2
The range defined has to represent a characteristic band of the sample (Amide I
at 1700 - 1600 cm-1). The first derivative is calculated and the maximum and
minimum absorbance values are determined. The difference between these two
values results in S1, a parameter which approximately corresponds to the inten-
sity of the band defined.
S1 is used to calculate the signal-to-noise ratio, i.e. S1 is divided by the noise

determined from the first derivative within a spectral range which shows no
absorbance bands (as defined in the x-Range 4). The minimum S1/Noise-ratio
value is indicated in the Signal/Noise entry field (value: 200).
S1 is also divided by the water vapor signal determined in the x-Range 5. The
minimum S1/WaterVapor-ratio value is indicated in the Signal/Water entry
field (value: 100).
x-Range 3
The range defined has to represent a second characteristic sample band (sugar-
ring vibration at 960 - 1260 cm-1). The first derivative is calculated and the
maximum and minimum values are determined. The difference between these
two values results in S2, a parameter which approximately corresponds to the
intensity of the band defined.
S2 is used to calculate the signal-to-noise ratio, i.e. S2 is divided by the noise

determined within a spectral range which shows no absorbance bands (as
defined in x-Range 4). The minimum S2/Noise-ratio value is indicated in the
Signal/Noise entry field (value: 40).
S2 is also divided by the water vapor signal determined in the x-Range 5. The
minimum S2/WaterVapor-ratio value is indicated in the Signal/Water entry
field (value: 20).

Evaluate
x-Range 4
The spectrum noise is calculated within a spectral range that shows no absor-
bance bands of the sample. (range: 2000 - 2100 cm-1).
In this range the first derivative is calculated and the maximum and minimum
values are determined. The difference between these two values is termed noise
and should not exceed the maximum value defined in the Noise max entry field
(value: 0.00015, i.e. 1.5 x 10-4).
x-Range 5
The water vapor intensity is calculated in a spectral range which indicates

severe water vapor symptoms but no sample absorbance (range:
1847 - 1837 cm-1). The first derivative spectrum is calculated and the maximum
and minimum vales are determined in the range defined. The difference
between these two values causes this huge water absorption. The value should
not exceed the maximum value defined in the Water max entry field (value:
0.0003).
x-Range 6
This spectral range is determined if the spectrum shows interferences (fringes).

The defined frequency range has to be free of any sample absorbance (range:
2200 - 2000 cm-1). The maximal difference between the highest and lowest
value of the first derivative is defined in the Fringes table line (value: 5 x 10-5).
9.9 Spectrum Search
OPUS offers several library search commands. For details, e.g. Library Editor
see the OPUS Search Manual which is part of the OPUS Search package.
The aim of spectrum search is to identify unknown substances. To perform a

search you need a library which is in line with your needs. BRUKER offers a
variety of commercial libraries which allow to solve many analytical problems.
You will find a free demo library on your OPUS CD containing 350 entries.
9.9.1 Starting a Spectrum Search

Select the Spectrum Search command and specify the spectrum files for the
search run on the Spectrum Search tab. If you check the Show Search Report
immediately checkbox, a report window displaying the results opens automati-
cally after the search run. You can limit the search also to an existing search
report. In this case only the substances listed in the report will be compared to
the test spectrum.

Spectrum Search
Figure 208: Spectrum Search
On the Search Parameter tab you define the desired search parameters.

Evaluate
Figure 209: Spectrum Search – Search Parameters
• Algorithm: BRUKER’s search algorithm uses a peak table together

with the experimental data (spectra). A temporary peak table is auto-
matically generated during a search using the “Standard” algorithm.
The second algorithm, “Use existing Peak Table” employs existing
peak tables, allowing one to suppress, for example, solvent peaks.
• Search Sensitivity: Using Search Sensitivity you can control the result
of your search. It is difficult to give a general recommendation for
the sensitivity value, because the search result depends highly on the
type of recorded spectra. For spectra taken from KBr pellets with a
typical Signal-to-Noise ratio, a sensitivity setting of 6 to 10 would be
reasonable. The best is, however, to learn about different sensitivity
settings by doing test runs applied to known substances. As a rule of
thumb, values higher than 15 rarely yield a significant result.
• Maximum Number of Hits: The number of hits that are to be saved in
the search report can be specified. Depending on the value set in the
Minimum Hit Quality field, the resulting number of hits can be lower
than this value.
• Minimum Hit Quality: This field is used to enter the minimum value
to qualify of a hit in the search. A value of 1000 would be a perfect
match, whereas a value of 0 is obtained in the case of no correlation
at all. In reality the search algorithm gives a value higher than 0 even
if no (or negligible) similarities exist between spectra. Therefore,
one restricts the number of hits included in the search report to a
lower limit (default settings 300). This value also depends on the

Spectrum Search
sample type and should be evaluated by measuring representative

samples. Only if a search yields no hits, should the Minimum Hit
Quality be set to a lower value.
You can limit the search to certain frequency regions of the spectrum instead of
comparing the whole recorded frequency range of the spectrum to the library
spectra. Enter either the frequency ranges manually in the table cells or use the
Interactive Range Selection button to directly select a frequency range in the
spectrum. Once you defined a list of regions to exclude you can save them
(Save Ranges as) for future use. Clear ranges clears the table and the Restore
last Ranges button automatically calls up the last range definition you used.
Figure 210: Spectrum Search – Exclude Frequency Regions
On the Select Library tab you select at least one library to apply for the search.
A search can involve either one or more libraries, but creates only one search
report.

Evaluate
Figure 211: Spectrum Search – Select Library
Use the Add Libraries and Remove Libraries buttons to include or exclude
libraries in the list. You can also save your library file selection for future use
and recall it using the Change List button. After loading a library list the library
files included in the list are marked by a small bullet.
Figure 212: Library File List
You can also test the integrity of a library file with the “Check Library” com-
mand. This command also updates the number of file entries. If a file passes
the test, it will be checked by a green mark.
Figure 213: Library Files – Integrity Test Passed

Spectrum Search
Problematic files are indicated by a red “x”. This can also be caused by the fact,
that OPUS cannot locate the library file (e.g. after you moved the file to a dif-
ferent directory).
Figure 214: Library Files – Integrity Test Failed
Corrupted files often are marked by an exclamation mark, usually accompanied

by an error message.
Figure 215: Library Files – Corrupted File
9.9.2 The Search Report

The result of a spectrum search will be saved in a report; you can read through
the report by opening a report window. The report will automatically be dis-
played if you checked the Show Search Report immediately box. Otherwise,
open the report by double-clicking on the report block.
The report window consists of four areas, which can be adjusted in size by mov-
ing the window bars. The list at the bottom of the window contains all spectra
matching the search criteria. The hits are numbered consecutively (first col-
umn) and sorted by hit quality. The first spectrum is selected (red square) and
automatically displayed in the display area above. The spectrum will only be
displayed if the box before the spectrum name is checked. To display the sub-
stance information and the structure, the spectrum must be selected. The hit
quality is marked before the name of the substance, followed by the entry num-
ber of the spectrum in the library.

Evaluate
Figure 216: Search Report – Results
Display the query spectrum by clicking on the Show Query Spectrum button.
Close the report window by clicking on Exit.
9.10 NeuroDeveloper Classification
For information on the NeuroDeveloper program, please refer to its extensive

online documentation.

Forward, Back
10 Display
The commands within this pull-down menu are for manipulating the display of
the active spectrum window. They allow you to zoom in on a detail of the dis-
play, and go back to the original display size. Some of the commands are not
always available, depending on the preceding steps performed. For example,
the Forward and Back commands are only active if you switched the display
magnification.
Figure 217: Display Menu
10.1 Forward, Back

Back allows you to restore the original display size on your screen after you
have zoomed in on a detail of the displayed curve. Forward will display the
zoomed in area again.
10.2 Stacked
If you loaded more than one spectrum into the same spectrum window you have
the option of a stacked display i.e. the spectra will not overlap. The preview
window is not affected by this command.

Display
Figure 218: Spectrum Window Containing Two Spectra – Normal and Stacked View
The ordinate will be duplicated when displaying two spectra in the stacked
mode. You can separate both spectra by displaying another abscissa, using the
Axis command of the spectrum window pop-up menu (accessible by right-click-
ing on the spectrum window). If you expand a part of one stacked spectrum, the
other spectrum will automatically be enlarged.
10.3 Scale All, Scale Y

You can fit a spectrum to the size of the spectrum window using the Scale All
command. If you only want to scale the ordinate, you can achieve that with the
Scale Y command.
10.4 Page Forward, Page Backward

If you have displayed only part of a spectrum you will see this part shown on a
white background in the preview window, while the rest of the spectrum which
is not shown appears on a gray background. You can move the displayed region
along the frequency axis using the Page Forward and Page Backward com-
mands. In this case you can browse a spectrum while keeping the displayed fre-
quency region the same.
10.5 Zoom In
The Zoom option allows you to choose the magnification. Use the left mouse
button to draw a frame around the region you would like to expand. After a sec-
ond mouse click the crosshair cursor disappears and instead you can reposition
the frame. Now left-click again and the area marked by the frame will be resized
to the spectrum window.

Windows Default Printer
11 Print
The Print menu contains the functions for printing spectra and reports. For
printing you can create and save templates to use with the Plot Layout Editor. A
conversion of OPUS-OS/2 templates is also possible.
Figure 219: Print Menu
However, before you can start to print your spectra you first have to define a
printer.
11.1 Windows Default Printer
11.1.1 Installing a Default Printer

The default printer is the printing device your computer addresses, if you don’t
specify another machine. To install a printer, you first have to connect it to the
parallel port of your computer or it must be connected to the network. For
details concerning the connection of the hardware, refer to your printers’ man-
ual. Next, install the printer driver:
• Open the “Printers” folder in “Setup”.
• Select “New Printer”. Windows will guide you through several dia-
log boxes, where you state the type of printer.
• Select this printer as the default printer, when asked.
• After the installation, a new printer icon appears in the “Printers”
folder.
11.1.2 Selecting the Default Printer

Ensure that a default printer is selected for your computer. Right-click on the
icon of the printer in the “Printers” folder. A pop-up menu appears in which the
“Set as Default” command must be selected.

Print
In the same menu, open the “Properties” dialog to switch to the scheduling
page. Select “Print directly to the printer”.
11.2 Defining Print Parameters
Use the Print Setup command from the Print menu to define the printer and the
print parameters like paper size and print quality. Clicking on the Properties
button opens another dialog box. The settings shown will depend on the model
and brand of your printer.
Figure 220: Print Setup
11.3 Print Spectra
Print Spectra uses a template to create a plot of spectra and all associated
parameters. Either drop a spectrum from the Browser onto the spectrum frame
or use the file selection list in the Print Spectra dialog. Use the Change Layout
button to select a template. Furthermore, if the template consists of several
frame types you can choose one using the pull-down list.

Print Spectra
Figure 221: Print Spectra
The Preview button opens another window in which a preview of the plot is dis-
played. If the plot consists of several pages you can choose between single and
double page display. In addition, you can magnify the displayed area.
Figure 222: Print Preview

Print
On the Options tab of the Print Spectra dialog the number of peaks to be
labelled and the scaling (autoscale or using the limits as specified in the tem-
plate) is defined. You can choose between a linear x-axis or an axis with com-
pressed wave numbers. In the latter case wave numbers above 2000cm-1 will be
compressed by a factor of two. Instead of a printout, the print job can be sent to
the clipboard.
Figure 223: Print Spectra – Options
11.4 Quick Print
You can use Quick Print to plot the contents of an OPUS view without specify-
ing a template. A default template suited for the currently displayed view
(located in the OPUS main directory) will be used. You can change these
default template editing it or by saving another template of your choice as the
default. The following templates are available:
Default Template Name Associated Window Type

3D.PLE 3D Window
3D+.PLE 3D+ Window
DEFAULT.PLE Display (spectrum) window
LIBRARY.PLE Library window
LIVE+OVERVIEW.PLE Live video and overview image window
LIVEVIDEO.PLE Live video window
MAP+SPEC.PLE Result window of a MAP acquisition

New Layout – Plot Layout Editor
OLDREPORT.PLE Report window

OVERVIEW.PLE Video overview window
ONLINE.PLE Result window of a CHROM acquisition
REPORT.PLE Report window
SEARCHRESULTS.PLE Search report window
SINGLEREPORT.PLE Report window
STRUCTURE.PLE Structure window
VIDEOPOSTRUN.PLE Video postrun window
The Quick Print command generates a printout showing the OPUS window as
is, i.e. in case you only displayed a part of the spectrum only this part will be
printed, including all labels and annotations.
11.5 New Layout – Plot Layout Editor
Use the Plot Layout Editor (PLE) to create templates used for multiple print-
outs. The templates you created can be saved using the Save as command from
the File menu. The PLE enables you to label peaks in a spectrum, plot details of
a spectrum, print parameters and peak tables.
Start the PLE by selecting New Layout from the Print pull-down menu. Now
the PLE tool bar becomes active and a new PLE window will be opened:
The PLE window consists of a black grid and a red frame. This frame represents
the available print area of your printer. Located next to the PLE workspace is
the PLE Browser. To the left of this window you find a column with the title
“item”.
The PLE window has a tab denoted “PE” attached. Use this tab to toggle
between the PLE and the spectrum window.
Since the available print area depends on your specific printer, its particular set-
tings must now be configured. If you have already installed a printer for Win-
dows, then you may skip the next section.

Print
OPUS Browser PLE Browser PLE tool bar PLE workspace Active frame
Figure 224: The PLE User Interface
• Start the PLE with New Layout from the Print pull-down menu.
• From the File menu choose the Print Setup command.
• The printers’ properties page will be displayed. Select the appropri-
ate paper size and format.
• Close the dialog box by clicking on OK.
• Now you can start your work with the PLE.
The OPUS Browser

The OPUS Browser lists all windows that are open, spectrum windows as well
as PLE windows. The active window is highlighted. You can switch between
windows by clicking on their icon in the Browser, or by clicking on the window
tab.
The PLE Browser

The PLE Browser lists all objects that are on the PLE workspace. A frame will
be referred to by the type of object it contains (table, spectrum etc.). The active

frame is indicated by a red arrow in the Browser and bordered by a thick line on
the PLE workspace. You can click on a frame to make it the active frame. This
can be useful, if the item is not visible because it is covered up or is outside of
the visible window area. You can right-click on an item in the Browser to bring
up its properties dialog.
Figure 225: The PLE Browser
The PLE Workspace

This is a visual representation of the printed page, containing all the frames.
Each frame can be scaled and positioned individually. A read-out below the
workspace gives you the exact position of the activated frame (left side), while
you move it around as well as size of the frame (right side).
Figure 226: Read-out for Frame Size and Position
By clicking on a frame with the right mouse key, you will bring up the Proper-
ties dialog box of this frame. Right-clicking the mouse on the page, in a portion
that does not contain a frame, will bring up the Page Properties dialog.
11.5.1 The PLE Tool bar
The tool bar allows quick access to the most frequently used PLE com-
mands. Select a tool by clicking on its icon before using it.
Draw a circle or ellipse on the page.
Draw a line or an arrow on the page.

Print
Draw a frame on the page. A frame can contain spectra, text, a bitmap or a
metafile.
Draw a frame that will contain a table.
The selection tool allows you to use the mouse to select and move items on
the page.
Add or remove a page. This allows you to create sophisticated templates

with more than one page.
Select page number.
Zoom factor (percentage). The zoom factor does not affect the size of the
templates’ printout.
Remove objects from the workspace. These objects have to be selected

before.
Clear a selected frame.
Open the PLE Page Properties dialog.
Anchor an object to its position on the workspace.
Open the PLE Box Properties dialog.
11.5.2 The Pop-up Menu

If you right click on a frame, a menu will appear at the point where the mouse is
clicked. This allows access to various actions, that can be performed on the
frame.
Remove deletes this frame from the workspace, while Snap to Grid aligns this
frame exactly on the closest grid lines. Insert Legend is only available to
manipulate spectrum frames and appends a legend to a spectrum frame.
Assign lets you change the content of a frame. You can assign pictures, meta
files, spectra, tables, text files or an OPUS view to a frame.

Copy duplicates the content of a frame or a page to a meta file or to a bitmap.
Figure 227: The PLE Pop-up Menu
Paste inserts a bitmap, a meta file or a text file from the clipboard into the
selected frame.
Edit manipulates the contents of a frame. This command is only available for
text and table frames.
Properties opens the dialog box associated to the selected frame.
Cancel closes the pop-up menu without performing any changes.
11.5.3 PLE Page Properties

Like all other objects the workspace itself has a property sheet associated with
it. Using the PLE Page Properties allows you to define general settings of the
PLE workspace. You call up this dialog box by right-clicking on the empty
space of the PLE page.

Print
(a) (e)
(b)
(f)
(c)
(g)
(d) (h)
Figure 228: PLE Page Properties
General Page Properties

(a) Specify the units that you want to work with (inches or centimeters).
(b) Select the orientation of the pages in the document.
(c) The available area for printing is represented by a dotted red line on the PLE
page. On account of the paper handling machinery of the printer, it cannot print
to the outermost edge of the paper. To determine the corresponding unprintable
area of the paper, check the manual of the printer or use empirical methods.
(d) Select the size of paper that is in the printer.
(e) This is the zoom (magnification) factor to use in viewing the PLE pages
expressed as a percentage. The typical computer screen is not large enough to
allow viewing the entire page at 100% scale. 75% is a good selection for docu-
ments using landscape orientation, while 50% is good for portrait orientation.
(f) This is the default font used in the document. As frames are created, they will
inherit this property. Once a frame contains data, the font can be changed for
that frame independently of this setting. This only determines what font will be
used when a frame is first created.
(g) The background color of the page.
(h) After you assigned the desired view type to the frame, i.e. a structure view, you
can drag & drop a structure data block onto the frame. To save the PLE page as
a template remove the data block again; the frame will retain the view type asso-
ciated to it. If the Interactive Opus view check box is marked, you can access an
object within a frame. You can assign any type of Opus view to a frame. Simply
draw a frame on the PLE page and right-click on it to open its Properties pop-up
menu. Selecting Assign Opus View will enable interactions with 3D spectra, e.g.
rotating the spectrum.

Grid Properties
(a)
(b)
(c)
(d)
(e)
Figure 229: Grid Properties
(a) This controls whether the grid is visible on the page. A grid is useful for align-
ing objects. However, the grid will not be printed.
(b) As objects are created, they can be automatically positioned and sized to line up
with the closest major grid lines.
(c) Usually a grid is displayed only on the screen because it is useful for alignment
during document composition. If you want the grid to also be printed on the
paper, select this option.
(d) This is the size of the grid, in the units that are specified in the Page Properties
page (above). The grid can be further divided by filling in the Minor fields.
(e) The color used to draw the grid.
Header and Footer Properties

The Header and Footer are information that are printed on the top and bottom,
respectively, of every page. The Header and Footer dialogs are identical, so
only the Header dialog is discussed. Everything said about the Header applies
to the Footer also.

Print
(a)
(b)
(c)
Figure 230: Header Properties
(a) The Header (or Footer) can consist of 6 fields: two rows in the left, middle, and
right. The entries in the fields consist of metastrings; you can either type them in
or drag them from the list (c). Of course you can also type plain text which will
be displayed.
(b) The font to use to print the Header (or Footer).
(c) These are special codes that the PLE uses to identify the information that will be
displayed on the page. You can use the mouse to drag the codes from the list to
the field that you want information to be printed in. Or, you can type them into
the fields directly.

Template Properties
Figure 231: Template Properties
You can also save a template to be used as default. When new PLE documents
are created, they will start with all of the properties of this template. The default
template is automatically named “default.ple” and is located in the same direc-
tory as the OPUS executable program. Using the Save As choice on the File
menu, templates can also be saved to any file name and directory. Using the
Open choice on the File menu, they can be recalled for later use.
11.5.4 Loading and displaying a spectrum

A spectrum can be loaded by simply dragging it from the Browser onto the
workspace. Alternatively, draw a frame by first selecting the icon and
then using the left mouse key. Open the frames pop-up menu by clicking on the
frame with the right mouse button, then select Assign and Spectrum. A file
selection box will appear, in which you may choose the spectrum you want to
insert. It will then show up in the frame, along with the axes and notation.

Print
Figure 232: Spectrum Frame
In order to print the parameters of the spectrum, select the icon from the
icon bar and draw a frame as done for the previous frame. This frame will con-
tain a table which has by default two rows and two columns. Again, change the
properties by calling up the Properties dialog (see chapter 11.5.6) with the right
button. The thickness of the dividing lines between the cells and the colors, as
well as the font, can be changed using the properties box. Also, you can assign
titles to the rows and columns.
Using the left mouse button select a parameter from the list on the second page
of the pop-up menu and move it to the cell in the table where you want it to
appear. The parameter will be displayed along with its value.
Figure 233: Table with Parameters Included
Text can be included using text frames, either typed in or by assigning a text file
to a frame. For manual text input draw a frame and open its pop-up menu. Use
the Change command to transform the frame into a text frame. A text field will
appear in which you now can enter the text. You close this field by left-clicking
anywhere outside the field. You can re-size the text frame as usual. By select-
ing Change again you can edit the text.

To import a text file start again by drawing a frame. From the Assign command
of the pop-up menu choose Text File. A file selection box opens from which
you can choose the text file to import. Currently, only files with the extension
“.TXT” can be imported. Text formatting is discussed in chapter 11.5.7
11.5.5 The PLE Spectral Frame Properties
The Item Page
(a)
(b)
(c)
(d)
(e)
(f)
(g)
Figure 234: Spectral Frame Properties – Item
(a) Change the size and position of the frame by entering the respective values in
the Size fields. The units used here are specified with the PLE Page dialog.
(b) You can select the line thickness used for the frame in pixels.
(c) The Color button lets you specify the color used to draw the frame, both, the
background color as well as the color of the frame. A color chart is displayed
from which you can either pick a color or define your own color.
(d) Normally, the border of the frame is not printed. Check this box if you would
like to have the border of the frame printed.
(e) Check this box to set the frames’ background color to the value chosen with (c).
(f) A name can be assigned to every object. Naming all the objects in your tem-
plate simplifies their identification in complex layouts. You can use these
names to link frames to each other.
(g) This field contains the target of a link operation. You can link table and text
frames to spectrum frames to keep your layout organized. To establish a link,
enter the Item Name of the target frame in the Linked To field.

Print
The Limits Page
(d)
(a)
(e)
(b) (f)
(g)
(c)
Figure 235: Spectral Frame Properties – Limits
(a) These are the limits for displaying the spectral data. The units are specified with
the PLE Page dialog.
(b) The style selected determines the presentation of the data in frame. You can
stack one spectra on top of another, or overlay them on top of each other.
(c) To add a Bruker Logo to your printout select this checkbox.
(d) Set the x limits (a) to the current outer limits of all the data that is in the frame.
(e) Set the y limits (a) to the current outer limits of all the data that is in the frame.
(f) When this option is selected the data is expanded to fill the area of the frame,
such that the axes coincide with the border of the frame.
(g) If this is not selected, only one spectrum at a time can be displayed in the frame.
The Axes Pages

The pages for x and y axis are identical except for the Rotate Numbers check-
box; this only exist on the y axis page. This function allows you to turn the
labels of the y axis by 90°. The Show axis for stacked spectra and the Com-
pressed Wave numbers checkboxes are only available for the x axis.

(a) (h)
(b) (i)
(c)
(j)
(d)
(k)
(e)
(f) (l)
(m)
(g)
(n)
Figure 236: Spectral Frame Properties – x Axis
(a) Controls whether the axes, tick marks, and labels are displayed.
(b) You can have separate x axes drawn for every spectrum of the stack. Otherwise,
one common axis will be used for all spectra.
(c) The Compressed Wave numbers command displays wave numbers above
2000cm-1 with a smaller linear scale.
(d) If automatic tick mark placement is not selected, this is the interval between the
tick marks.
(e) If automatic tick mark placement is not selected, this is the position of a tick
mark.
(f) If automatic tick mark placement is not selected, this is the number of decimal
places used for the numeric tick mark labels.
(g) The label to display on the axis. This is automatically taken from the data file as
data is loaded, but can then be changed by editing this field.
(h) Selecting this allows the PLE to alternatively determine where the tick marks
are placed.
(i) If you want tick marks on top of the data area, select this.
(j) If you want the tick marks displayed at the bottom of the data frame, check this.
(k) The thickness of the axis line.
(l) The color to use for drawing the axis.
(m) The font to use for the axis label.
(n) The font to use for the tick mark (numeric) labels.

Print
Data
(c)
(a)
(d)
(e)
(b)
(f)
Figure 237: Spectral Frame Properties – Data
(a) As data is added to a spectral frame, it is put into a “slot”, which is just a posi-
tional number. To change the look of the data in the slots, select the slot in this
list box. Then define the properties for that slot, using the rest of the controls on
this dialog: Color, Line Type, and Line Width.
(b) Remove the data that is selected in the list (a) from the frame.
(c) The color to use for displaying the data selected in list (a).
(d) The line style to use for displaying the data selected in list (a).
(e) The line width (in pixels) to use for displaying the data selected in list (a). Sep-
arate widths can be specified for the screen and the paper.
(f) In case you included annotations in your spectrum you can have them printed
with the font selected via the font dialog box (Font.. button) if you place a mark
in the Annotations checkbooks.

Peaks
(e)
(a)
(f)
(b)
(c) (g)
(d)
(h)
Figure 238: Spectral Frame Properties – Peaks
(a) Similar to the Data page the slot holding the relevant data has to be selected
first.
(b) Select the stroke line thickness in pixels for the display and the printout.
(c) Label Font lets you control the font type used for the stroke labels.
(d) Change the color of the strokes using Stroke Color.
(e) Checking this box ensures extra space between the highest peak and the spec-
trum frame for the peak labels resulting from a peak search. The label type can
be chosen from the list (f).
(f) Select the type and position of the labels you want to assign to the peaks.
(g) Specify the number of peaks to be labelled, starting with the highest peak.
(h) Set the number of digits and decimals of the peak labels.
11.5.6 The PLE Table Properties

A table is created by choosing the “Table” drawing tool on the PLE tool bar,
and then drawing it on the page using the mouse. Tables are linked to spectrum
frames via the Item Name and Link To fields on the Item tab (discussed above).
By default, a table of two columns and two rows is created. The number of col-
umns and rows can be changed by right-clicking on the table and opening the
corresponding Properties dialog box.
Cells in a table can also be edited manually, by right-clicking the mouse over
the cell and selecting Edit from the menu that appears. When you are editing
cells, you can navigate between them using the arrow keys. The return (Enter)
key also switches the editing to the next cell in the column.

Print
The first tab of the Table Properties dialog has been already discussed in
chapter 11.5.5.
Parameters
(a)
(b)
(c)
(d)
Figure 239: Table Properties – Parameters
(a) The available parameters are categorized. Depending on the category selected,
the information displayed in the list box (b) will change.
(b) Available parameters of the type specified in (a) are listed here. To add informa-
tion to a table, select an item from this list and then drag it to a cell on the table,
and drop it there. The strings here are metastrings: a three letter code preceded
by a “^” character. When PLE encounters such a code, it interprets it as an
instruction to extract the information from data slot one of the linked spectral
frame and substitutes that information for the code, when the table is displayed.
If you edit the cell (via the Edit choice on the context menu, below), you will see
the actual codes. When the table is displayed, you see the information that the
code symbolizes. If you do not like the default format of the information, just
edit the cell and change it.
(c) Normally, the information extracted by PLE to expand the metastrings is taken
from the spectrum in slot one of the linked spectral frame. By choosing this
option, the parameters can be repeated for each spectra in a frame, up to the
number of rows you have defined on the Format dialog (below).
(d) As new spectra are added to a frame, new rows can be added to the table to dis-
play the parameters for each spectrum. This setting will override the number of
rows that you have set on the Format dialog (below).

Format
(a) (h)
(i)
(b)
(c)
(k)
(d)
(l)
(e)
(f)
(m)
(g)
Figure 240: Table Properties – Format
(a) The number of columns in the table; the default value is two.
(b) The number of rows in the table; the default value is two.
(c) The font to use for row 1 (if the Row 1 has titles option is checked).
(d) A grid can be displayed, which contains each cell in the table.
(e) The thickness of the grid, in pixels.
(f) Cells can be sized automatically to fill the frame that encloses the table.
(g) If Autosize is not selected, this is the height of a cell (in the units specified to the
right (l)).
(h) If this is checked, the text in column 1 is used as a column header, and is dis-
played in the font specified using the Title Font button (c).
(i) If this is checked, the text in row 1 is used as a row header, and is displayed in
the font specified using the Title Font button (c).
(j) Assigns different colors to better distinguish the rows.
(k) The font to use for the body of the table. If Column 1 has titles and Row 1 has
titles are both unchecked, this font will be used for every cell in the table.
(l) The color of the grid, if it is to be displayed. After a selection has been made
this button will be displayed in the color of choice.
(m) If Autosize is not selected, this is the width and height of a cell (in the units spec-
ified to the right).

Print
11.5.7 The PLE Text Properties

If a frame contains text, its properties can be set here. The text can consist of
metastrings or manually typed characters. The metastrings used for table param-
eters (see chapter 11.5.6) can also be typed into a text frame, and they will be
interpreted by PLE using the data from the spectrum frame linked to the text
frame.
The Item and Parameters tabs have already been discussed in the previous
chapter.
(a)
(b)
(c)
Figure 241: Text Properties – Text
(a) Defines the tab stops for the text in the frame. Multiple positions can be used,
separated by spaces, such as “8 12 20 40”. The last tab spacing is used for subse-
quent tabstops, should more be contained in the line.
(b) The font and font size to use for the text.
(c) Centers the text within the frame.
11.6 Open Layout
New Layout calls up the Plot Layout Editor, while Open Layout shows a list of
existing templates. When using this command for the first time after the instal-
lation of OPUS you will have to navigate to the desired directory.

Print / Print Preview
11.7 Print / Print Preview
You can view the result of a printout using the Print Preview command. Print
will start the printing process immediately.
11.8 Print Setup
Paper orientation and the printer (in case you have more than one printer
attached to your computer) are selected using the Print Setup menu.

Print

Script Recorded History
12 Macros
OPUS functions you use routinely, can be automated as a macro. An OPUS
macro is a sequence of OPUS commands that can be executed as one unit.
Besides the regular OPUS commands a set of macro functions exists to control
the macro execution, the interaction with the user and the evaluation of results.
An OPUS macro basically is a text file with the extension “.MTX”, which can
be edited using any kind of text editor. A detailed description of all macro func-
tions and the command language is given in the “OPUS Programming” manual.
This chapter briefly describes the commands of the Macro pull-down menu. It
also tells you how to include macros in the OPUS tool bar.
Figure 242: Macro Menu
12.1 Script Recorded History
The information stored in the history block of a file can be extracted into a
script. Select the file you want to extract the performed manipulations from and
load it into the upper window. Select a file name for the script and define the
path, where it should be saved to. Include Measurement includes the measure-
ment parameters as well.
Once the script has been saved, it can then be carried out on other files using the
Visual Basic Scipt function from the File menu.

Macros
Figure 243: Macro Menu
12.2 Macro Converter
Use the Macro Converter to translate macros written under OPUS-OS/2 into the
OPUS format. The conversion may require some changes as a result of the dif-
ferent macro syntax. See the “OPUS Programming” manual for details.
12.3 How to Run a Macro
To run a macro use the Run Macro command of the Macro pull-down menu.
The file load box appears through which you can immediately start the macro
you have selected. All further action depends on the macro you have chosen.
12.4 Debugging a Macro
The term “Debugging” means a step-by-step execution of a macro program

with the aim of locating program errors. The program execution will continue
until a stop mark is reached. This option greatly facilitates locating and analyz-
ing errors.
12.5 Macro Editor
OPUS includes an editor to conveniently generate and edit your own macros.
Start the editor with the Macro Editor command from the Macro pull-down
menu. Either generate a new macro or load an existing one by clicking on the
Open Macro button.

Compiling a Macro
12.6 Compiling a Macro
Macros are written and stored as text files, which will be converted to execut-
able binary code during runtime of the macro. The Compile function performs
this step separately and generated executable binary code from a macro text file.
Compiled macros are started faster than macros in text format.
12.7 Adding a Macro to the Toolbar
Macros which you use regularly can be added to the toolbar. To do this you
have to add an entry to the USERMAC.LST file, to be found in the OPUS direc-
tory. If this file does not exist on your machine it has to be created using a text
editor.
For every macro you want to include in the pull-down menu of the tool bar you
have to add the following information to the USERMAC.LST file:
1) Name and path of the macro file.
2) Number of the menu (see table).
3) Text to be included in the menu.
4) Text for the tool description of the tool bar.
5) Text for the status bar.
Separate the entries by an “@” sign, e.g.:

E:\OPUS\MACRO\IT.MTX@8@Instrument test@IT-Test@Start IT
If you want to include an icon for the macro added to the tool bar you have to
provide a 16*15 pixel bitmap. This bitmap must reside in the same directory as
the macro.
To specify the menu you want to add a macro to, use the number indicated in
the table.
Menu Number of Menu
Measure 1
Manipulate 2
Evaluate 3
Display 4
Print 5
Macro 6
Edit 7

Macros
Validation 8
Settings 9
File 10

Instrument Test
13 Validation
The Validation menu consists of two items, the Instrument Test to ensure maxi-
mum performance of the instrument and a function, where you can add signa-
tures (when the OPUS package 21 CFR part 11 was purchased) and the
Methods, where you can display the history of methods.
13.1 Instrument Test
The test comprises the following features:

• Check of the Signal-to-Noise Ratio
• Recording a 100% line
• Interferogram amplitude check
• Source check
• x axis calibration
• Check of the y axis (reproducibility of a glass filter spectrum)
The test status will be displayed in the status line and several dialog boxes,
while the Instrument Test is running. When the test is finished the result will be
written to an ASCII file labelled ITDate of Test.txt. You can open this file using
a standard text editor like Notepad. Alternatively, have the file printed by
checking the Print Result checkbox on the first page of the Instrument Test
(Fig. 245).
Figure 244: Validation Menu
Every run of the Instrument Test is documented in a log file called “IT.LOG”,
including the date and time the test was performed, the operator name and the
test result.

Validation
Figure 245: Instrument Test – Parameters
Before you setup the Instrument Test, got to Optics Setup and Service in the
Measurement menu and check the item Channel Specific Laser Wave number on
the page Interferometer/AQP.
If you run the test for the first time choose Setup IT to adjust the laser wave-
length and acquire a set of reference spectra.

Instrument Test
Figure 246: Instrument Test – Main Page

Validation
Figure 247: Instrument Test – Setup Page
Choose Set Instrument and specify, whether you want to have the x and y axes
checked, by marking the respective boxes, and which tests (polystyrene or water
band calibration) should be applied.

Instrument Test
Figure 248: Instrument Test – Set Instrument Page
In order to adjust the laser wavelength, a high resolution single channel spec-
trum of the water band is acquired. For comparison, the following peak posi-
tions are used:
MIR: 1554.353 cm-1

NIR: 7306.74 cm-1
The HeNe laser operates at a wavelength of 15798 cm-1; if the observed wave
number of the water peak deviates from its theoretical value, the value for the
HeNe wavelength has to be changed until the experimental value matches the
theoretical value. Apply the change by clicking on the button Set Laser Wave-
number.
Next, acquire the reference spectra set. This step should always be performed
after adjusting the laser wave number. The reference spectra are measured with
and without a glass filter and stored in the files ENERGY.0 and GFA.0 (and
GFB.0, if required). Click on Measure Reference Spectra.

Validation
Figure 249: Instrument Test – Adjust Laser Wave number
After completing the setup, the Instrument Test can be started. Click on
Start IT. While the test is running, its status will be displayed in the status bar.
The test result will be displayed as OK or NOT OK. In case of a negative result,
you can save the test report on disk for future analysis.

Instrument Test
Figure 250: Excerpt of an Instrument Test Report

Validation
13.1.1 Signal-to-Noise Ratio

The Signal-to-Noise Ratio is tested in the frequency range which is specified in
the Acceptance Measurements of the BRUKER service department. The Sig-
nal-to-Noise Ratio is calculated in the Peak-to-Peak mode by fitting a parabola.
The limit for the Signal-to-Noise Ratio depends on the instrument type and the
experimental configurations. If you use for example the internal measurement
channel of an IFS 28N the limit is 10000 (NIR diode), while if using a Y fiber
the limit would be 800.
13.1.2 Test 100% Line

The maximum deviation of a transmission spectrum (without sample) from
100% Transmittance is recorded. The frequency range considered for this test is
larger than the interval taken to determine the Signal-to-Noise Ratio. In case of
a NIR diode frequencies ranging from 10000cm-1 to 4300cm-1are used. This
tests mainly short term stability of the instrument.
13.1.3 Interferogram Peak Amplitude

When performing a reference measurement the energy throughput (empty beam
path) is measured and stored in the file ENERGY.0. Both, the interferogram
and the single channel spectrum are stored. This reference file should only be
acquired after the alignment of the spectrometer optics.
When running the Instrument Test the same measurement is repeated and the
result is compared to ENERGY.0. The amplitude of the reference interfero-
gram is set to 100% and the amplitude of the test interferogram is compared to
this value. The ratio is included in the Instrument Test report. This test reflects
the long term stability of the instrument.
13.1.4 Checking the Source

This test evaluates the integral of the intensity over the total frequency range of
the reference spectrum ENERGY.0. This value is then referenced against the
value obtained from ENERGY.0. The deviation of both values increases as the
spectrometer source wears out. The reference spectrum ENERGY.0 should be
renewed after changing the source.
13.1.5 x Axis Calibration

In order to test the frequency calibration a polystyrene standard sample can be
used. The film should be about 1mm thick when used in the NIR region and
about 50µm to calibrate in the mid-IR. Most of the instruments are delivered
with these standard samples included.

Methods - Add Signature/Show History
Alternatively, the absorption bands resulting from water vapor (1554.353cm-1

and 7306.74cm-1) can be used to reference the x axis. These peaks are more
narrow than the signals obtained from a polystyrene sample. If your spectrome-
ter is equipped with a Ge detector you have to use the water vapor bands for cal-
ibration because polystyrene has no suitable absorption in the frequency region
of this detector.
13.1.6 y Axis Reproducibility

A transmission spectrum obtained from a glass filter is used to test the precision
of the y axis. The same spectrum has been acquired during the reference mea-
surement. When re-running this test the average deviation between test and ref-
erence spectrum is calculated over a large frequency range. The actual width of
this range depends on the type of your instrument. The range limits are stored
in the IT_GF.INT file.
13.2 Methods - Add Signature/Show History
With the “OPUS 21 CFR 11“ package installed, signatures can be added here.
For further details, see the 21 CFR 11 manual. Without the package installed,
you are still able to view the history of methods created beforehand.
Figure 251: Methods - Signature

Validation
Go to the Signature page to select the method you would like to review. When
the method is loaded, switch to the History page to see the history of the
selected method.
Figure 252: Add Signature/Show History - History page

Logout
14 Setup
Figure 253: Setup Menu
14.1 Logout
To login a new user or to logout and terminate OPUS chose Logout from the
Setup menu.
Figure 254: Logout Screen
To log in, choose the User ID from the combo box. The last user is always
shown. Enter the proper user password. The password is displayed as a series of
“*”. The user type (Operator or Administrator) for the currently selected user is
displayed.
Choose one of the workspaces from the combo box. The contents of the combo
box depends on the selected user. In case of Operators only the assigned work-

Setup
spaces are shown while in case of Administrators all workspaces in the OPUS
root directory are shown. Click on the "Login" button to log in the new user.
Click on "Exit from OPUS" to cancel the login procedure and leave OPUS.
14.2 Setup JCAMP/OPUS Conversion

Use this command to set the conditions for the conversion of JCAMP files into
OPUS files. To avoid the loss of information conversion tables are used to cor-
relate JCAMP labels with OPUS parameters and information. These tables are
text files with the extension “.PCT” which can be generated using any kind of
text editor (see below). In addition, the file containing the infotext definition has
to be stated. Use the Change buttons to browse the directory for the files that
hold the desired conversion tables.
Figure 255: Selecting Conversion Tables
“.PCT” file Syntax:
#Ixx:yyy:LABEL
Ixx the number of the line in the info block, xx being a two-digit number
starting with 01; this number, followed by a colon is mandatory.
yyy a three character OPUS parameter, optional.
LABEL the name of the JCAMP label, optional.
Example (DEFAULT.PCT from the \OPUS\methods directory):

#I01::SNM:TITLE
#I02::MOLFORM
#I03::MW
#I04::CAS REGISTRY NO
#I05::MP
#I06::BP
#I07:SFM:SAMPLING PROCEDURE
#I08::
#I09:CNM:ORIGIN
#I10::CROSS REFERENCE

User Management
#I11::CHARGE NO
#I112:HIS:DATA PROCESSING
14.3 User Management

PC’S running OPUS as the spectrometer software may be used in companies/
institutes which are legally bound to quality regulations.
One essential part of such regulations is the access control to computer systems
and any kind of software. While the operating system itself grants a high level
of access control to the computer system itself it might be desirable to have
another level of access control to a software package itself. This allows to install
a group security for more than one operator for the operating system but indi-
vidual access configurations for the application software so that more than one
user can work with the software without the need to reboot the system each time
a different user wants to access a certain software package.
Definitions
User Database: A database with different User Records
User Record: An entry in the User Database, specifies User ID,
User Name, Password, User type, Workspaces
User ID and Password:Is required for logging into OPUS
User Name: Is the name stored in measured spectra and shown
in all audit trails
User Type: Specifies the access rights of a user
Workspace: User environment within OPUS
Assigned Workspaces: Workspaces which can be used by a certain user
Default User Database

To allow immediate access to a newly installed OPUS a default User database is
installed automatically. A single user record is predefined in this default data-
base which allows full access to OPUS and all workspaces. The User Data of
this record are:
User ID: Default

Password: OPUS
User Name: Default
User Type: Administrator
Assigned Workspaces: Unlimited access to all workspaces
We recommend not to delete this user record and to change the password if you
are going to use the features of User Management.

Setup
Setup of User Records

Note: User Records can only be created, modified or deleted by operators who
are logged into Windows as User with administrator rights. Otherwise the func-
tion is not accessible in OPUS!
After selecting User Management from the Setup menu the following dialog is
shown.
b
c
d
g
e
f
k l
Figure 256: User Management - Administrator
a) Buttons to scroll through the different user records.

b) Enter the User ID for the user. The User ID must have a minimum length which
can be specified on the "Global Options" page. The User ID is required for the
OPUS login.
c) Enter the password for the user. The password must have a minimum length
which can be specified on the "Global Options" page. The password is required
for the OPUS login. The entry in the password field is shown as a sequence of
"*".
d) Re-enter the password for verification. The entry in the password verification
field is shown as a sequence of “*”.
e) User name. This name is stored in newly measured spectra and in the audit trail
of spectra and methods.

User Management
f) The user type can either be Administrator or Operator. An Administrator has

access to all OPUS workspaces while an Operator only can use assigned work-
spaces (see below).
g) Password duration (if any). The password duration can be specified on the "Glo-
bal Options" page
h) (see dialog below) List of workspaces. This list shows all workspaces which can
be accessed by the user. This list is invisible for users with Administrator rights
because administrators have unlimited access to all workspaces.
i) (see dialog below) Use this button to add a workspace to the list. Workspaces are
always stored with full path. If you move a workspace to a different path you
will no longer have access to it.
j) (see dialog below) Use this button to remove the currently selected workspace
from the list.
k) Option to lock a user. The exclude flag is automatically set if a user tries to log in
with a wrong password several times. The number of tries can be set on the "Glo-
bal Options" page.
l) Button to delete the current record.
m) Store all records in the data base.
i j
Figure 257: User Management - Operator
The total number of user records is shown in the top line of the dialog box. The
number of the current user record is shown between the two scroll buttons.

Setup
All entry fields which must be filled are initially marked red. When you start
typing in any of the red entry fields the color of the entry field changes to yel-
low after the first character has been typed in. The color of the input field stays
yellow as long as the number of typed characters is lower than specified for the
current field. If the minimum number is reached the color changes to white indi-
cating a valid input.
The default settings for the different fields are:
User ID 3 characters
Password 4 characters
The default settings can be changed on the "Global Options" page and will
immediately influence all user records.
The Password Verification field will only change to white if the text entered in
that field is identical with the text entered as password. The password can be
empty if the appropriate option is selected on the "Global Options" page. In this
case the Password field is initially yellow and the Password Verification field is
white.
Duplicate User IDs or duplicate First and Last Names are not allowed and will
be indicated by red entry fields.
The Password Verification field will only change to white if the text entered in
that field is identical with the text entered as password.
The password can be empty if the appropriate option is selected on the "Global
Options" page. In this case the Password field is initially yellow and the Pass-
word Verification field is white.
Duplicate User IDs or duplicate First and Last Names are not allowed and will
be indicated by red entry fields.
It is not possible to store the signature records unless all obligatory fields
have been filled properly. For users with Operator rights at least one work-
space must be in the workspace list.
The user records are stored in a file USERDATABASE.DAT in the USERDA-

TABASE sub directory of OPUS. The file is encrypted and can thus not be
modified externally. We highly recommend to protect this file against deletion
for all users using the security options of Windows and to make a backup copy
whenever you modify this file but you must not set this file to read only!
The next page of the dialog, the Global Options for the User Management can
be set.

User Management
a
b
Figure 258: User Management - Global Options
This page allows to specify

a) The minimum length of the User ID.
b) The minimum length of the password.
c) When this check box is checked, empty passwords are allowed. Please note that
independent from the password duration setting empty passwords will never
expire!
d) This checkbox switches the password duration option i.e. the password never
expires or it expires after the specified number of days.
e) Password duration in days. This field is only visible if the password duration
option is set appropriately. The duration period starts with the date the user
record is created or modified.
f) Maximum number of illegal login attempts i.e. during login the entered pass-
word is wrong. The user is getting an warning which tells him how many tries
are left. If the last try was also unsuccessful the user will be locked and will no
longer be able to run OPUS. Only the Administrator can remove this lock.
Changes of the settings apply immediately to all user records in the data base.
Therefore you must check all user records after modification of any of the
options. Illegal entries will be marked as already described above.
The third page of the dialog shows the audit trail of all actions for each user.
The following events are recorded:

Setup
Successful Login
Login attempt of a locked user
Login with expired password
Password change
A global audit trail (user index 0) shows all login attempts of unknown users.
Figure 259: User Management - Audit Trail
a) Buttons to scroll through the user records and the global record
b) Audit trail
c) Button to delete the currently shown audit trail
14.4 Change User Password

Each user is allowed to change his password. Reasons for changing a password
can be different:
• A new user record has been entered. In this case the administrator
enters the initial password and the user might want to change it.
• The Password Expiration option is enabled and the password is
expired after the specified period of time. In this case the user can no
longer login into OPUS (see below).

Change User Password
• A user fears that someone else knows his password.
In order to change a password within OPUS the user must call the "Change User
Password" function. The "Change Password" dialog appears.
b
c
Figure 260: Change User Password
a) User name and User type.

b) Entry field for the new password
c) New password verification
d) Store new password in User Record
Please note that the new password must be different from the old one and must
have the minimum length set up by the administrator.
If your password is already expired when you attempt to start OPUS you will
see a warning message after you have tried to login. The dialog then changes
and allows you to enter a new password.
Figure 261: Change Expired Password
The same rules apply as for the "Change Password" function described above.
After the password has been changed the login dialog appears again. You can
now login into OPUS with the new password.

Setup
14.5 Setup User Macro List

This function can be used to integrate macros or VB-Scripts into OPUS. The
user own macros/scripts are integrated in the menu and can be added to the tool-
bars. It is possible to add macros/scripts in different languages.
a
b
d
e
g
i
k
h
l
j
Figure 262: Setup User Macro List
a) Select the language for the entry. The default language is the language in which
OPUS was started. Only the entries for the selected language can be edited.
When the language is changed the entries for the newly selected language are
accessible.
b) Shows the total number of entries and the number of entries for the current lan-
guage
c) The navigate buttons allow to scroll between the different entries for the current
language
d) The menu where the macro/script shall be added to can be selected from the
combo box.
e) Use the browse button to select the macro/script for the entry. To prevent errors
the path and name of the macro/script cannot be entered manually.
f) Three different text fields have to be specified: The text shown in the menu, the
text shown as tooltip and the text displayed in the status bar
g) This button deletes the current entry from the list
h) An entry can be copied into the list for a different language by clicking on that
button. After copying an entry the language can be changed in A and the entry
can then be translated or otherwise modified.
i) This combo box specifies the target language for copying. Copying into the same
language as specified in A is not possible.
j) This button stores all entries for all languages in the USERMAC.LST file

Register OPUS
k) Exit from the function without storing any modifications

l) Shows the online help for this function
Contents of the USERMAC.LST File

The USERMAC.LST file in the OPUS directory is stored as a plain text file.
[ENGLISH]
.\macro\it.mtx@8@Instrument Test@Instrument Test@Run the Instrument Test
[GERMAN]
.\macro\it.mtx@8@Gerätetest@Gerätetest@Gerätetest durchführen
[FRENCH]
.\macro\it.mtx@8@Test d'instrument@Test d'instrument@Lancer le test
d'instrument
The key words in square brackets specify the different language sections.
Within the sections each line represents a macro/script. The different parts of
the lines are separated by the "@" character. The different parts have the follow-
ing meanings:
.\macro\it.mtx@8@Instrument Test@Instrument Test@Run the Instrument Test
(1) ( 2) (3) (4) (5)
(1) Path and filename of the macro/script

(2) Menu number
(3) Text for the menu
(4) Text for the tool tip
(5) Text for the status bar
14.6 Register OPUS

After installing OPUS you can test the program for 30 days without registering.
After this trial period you have to register your copy of OPUS. Furthermore,
you can use libraries and additional OPUS packages only after you have regis-
tered your copy. To register you have to obtain the necessary information (key,
serial number etc.) from Bruker. The registration has to be only performed once
and is valid for all users of the system. You must be a Windows power user to
register.

Setup
Figure 263: Registration Dialog
The key will be only visible while you type, later on it will be masked. The
serial number of OPUS and the OPUS library consist of numbers only. The key
also includes characters; be sure to type capital letters when required.
After registering OPUS these fields will be grayed out unless the Change Regis-
ter Fields checkbox is marked. When you buy additional OPUS packages or
libraries you may have to re-enter some of the information in order to use these
packages.
14.7 Customize Tool bars

You can personalize your OPUS workspace by configuring the tool bars to suit
your requirements. Open the Customize Tool bars command of the Setup pull-
down menu. Alternatively, right-click on the empty space of a tool bar to obtain
the dialog box.

Customize Tool bars
Figure 264: Customize Toolbars
You can:
• move bars with the mouse.
• generate new bars or load existing bars.
• use the Show Tooltips checkbox to display help texts.
• turn separators on and off (New Look).
• include descriptions in the icon (Large Buttons).
Add or remove icons to a tool bar using Commands page of the Customize Tool
bars dialog box.

Setup
Figure 265: Customize Toolbars – Commands
14.8 Customize Menus

Like the tool bars you can also customize the pull-down menus. By default the
Show All Functions checkbox is marked during the OPUS installation. As a
result the menus include all available OPUS functions. However, you can create
your personal profile (if your rights according to 21CFR11 allows a customiza-
tion of the workspace) by choosing the functions you wish to use.

Customize Menus
(a)
(b)
(c)
(d)
(e)
Figure 266: Menu Settings
To customize the menus first remove the tick from the Show All Functions
checkbox (e), which is selected by default. Select the menu you want to config-
ure from the menu list (a) and then add the functions you would like to include
by selecting them from the Available Functions list (b). Use the Add Selected
button to include them in the Functions list (c). You can change their order of
appearance in the menu with the Up and Down buttons and add separators to
structure the menu.
Your individual settings will be saved in your user profile. However, you can
only customize your profile when you were granted the necessary rights to do
so.
You also can use the Menu Settings to configure the display pop-up menu. To
do this, remove the tick from checkbox (e) and choose Display Popup from the
list (a). Add the functions you would like to include in the pop-up menu and
check box (e) again.
Shown in Figure 267 is the display pop-up menu in which three functions have
been added. To facilitate the identification of these functions they have a small
tag on the left side.

Setup
Figure 267: Display Pop-up Menu with Added Commands
14.9 Display Settings

Change the appearance of the spectrum window by calling up its pop-up menu.
This is discussed in chapter 2.3.
14.10 User Settings

Create and manage OPUS user profiles with the User Settings dialog. How-
ever, to do so you must have been granted the necessary rights. On the first
page of the dialog you can see who is logged in as user. In the bottom half of the
page, state the path for the most frequently used OPUS directories.

User Settings
Figure 268: User Settings – General
On the 21CFR11 Rights page assign the rights for the current profile. Here you
can select whether to work in GLP mode (and save the original data) or not.
Keep in mind that at least one administrator profile possessing all rights should
exist.
Figure 269: User Settings – Assigning Rights to Profiles
On the Preferences page select the type of file name incrementation. You can
either have the file name incremented or its extension. Furthermore, in the bot-
tom half of the page, you can set the number of digits for frequencies and inten-
sities to be displayed in the report.

Setup
Figure 270: User Settings – Preference
On the Display page, you can set the default display limits and chose whether
the axes should have legends. Furthermore, tick the right box if you want to
have arrows with your annotations.
Figure 271: User Settings –Display
On the Diagnostics page, tick, which warning indications or alarms you want to
set for your instrument:

New Workspace
Figure 272: User Settings – Diagnostics
The Instrument Test page enables you to set the path where the IT methods are
stored.
Figure 273: User Settings – Instrument Test
14.11 New Workspace

OPUS is able to manage several user profiles which can be password protected.
A profile contains information OPUS about the users rights, his customized
desktop (tool bars, menus), the parameters of all commands as well as the users
name and password. Create a new profile with New Workspace. See
chapter 14.10 for details.

Setup
14.12 Save Workspace as

If you changed anything concerning the settings saved in your profile, e.g. the
position of the tool bars, your profile will automatically be updated when you
exit OPUS. If you created a new profile OPUS will ask you for the profiles
name.

Getting Help
15 Miscellaneous
15.1 Getting Help
Figure 274: OPUS Help Menu
OPUS provides Help topics, either available from the Help menu or by clicking
on the Help button of a dialog box, and the manuals as “PDF” files. The online
help can also be activated using the F1 button of your keyboard. To use the
online help function you have to install Microsoft Internet Explorer 4.0 (or
higher). In order to read the “PDF” files the Acrobat Reader, which is included
on the OPUS CD, must be installed.
15.2 Setting the Language
During installation you have the choice between three languages, English,
French and German. Nevertheless you can force OPUS to use the language of
your choice at any time. Start OPUS from the command line or create a short-
cut using the following commands:
• OPUS/LANGUAGE=ENGLISH starts the English language module
• OPUS/LANGUAGE=FRENCH starts the French language module
• OPUS/LANGUAGE=GERMAN starts the German language module
Make sure to type the command in capital letters. If the command is not recog-
nized, OPUS will use the default language, which is English.
Figure 276 shows how to include the language command in an OPUS shortcut.
Right-click on the Windows Start button and choose Open All Users. Right-
click on the OPUS shortcut icon and open its properties sheet.

Miscellaneous
Figure 275: Selecting OPUS Shortcut Properties
On the Shortcut page add the command for selecting the language in the target
line. Next time you start OPUS using the shortcut, the specified language will
be used.
Figure 276: Properties Sheet of OPUS Shortcut

Rebooting the AQP
15.3 Rebooting the AQP
Sometimes it may be necessary to reboot the acquisition processor. A simple

way to reboot is to change any of the configurations in the Optics Setup and
Service menu. Every change of these parameters (e.g. changing the optical
bench and back) causes the AQP to reboot.
15.4 Abort OPUS
If your computer hangs while executing OPUS you can end the program with
the Windows Task Manager. However, be sure that OPUS is not in the midst of
processing a command, which may give the impression that OPUS quit react-
ing. All changes you have made during the session which you did not save up
to now will be lost when you abort OPUS. To call up the Task Manager, press
the Alt, Control and Delete keys at the same time. This will open the Task
Manager window. Now select OPUS from the Applications page and click on
End Task. OPUS will terminate without saving any data. Be careful not to
abort any other program, this may cause your system to become unstable.
Figure 277: Windows Task Manager

Miscellaneous

Appendix
Data Block Icons
OPUS files consist of several spectra, reports and result blocks; these will all be
combined using the same file name.
a b c d e f g h i j
1
Sometimes data blocks are referred to by their name, e.g. by the Browser or in
macros. The following list contains the data block names and a short descrip-
tion.
1a single channel spectrum, reference ScRf
1b report Report
1c reflectance spectrum Refl
1d Raman spectrum Raman
1e Quant report Quant
1f Quality test QTest
1g sample, power spectrum PwSm
1h reference power spectrum PwRf
1i sample, phase spectrum PhSm
1j reference, phase spectrum PhRf

2a unknown block
2b peak table Peak
2c photoacoustic spectrum PAS
2d n th derivative n.Der
2e logarithm of reflectance lgRefl.
2f Kubelka-Munk spectrum KM
2g integration report Integ
2h information block Info
2i sample, interferogram IgSm
2j reference interferogram IgRf
3a protocol History
3b transmittance spectrum TR
3c video image Graphics
3d general report GenRep
3e fit report Fit
3f emission spectrum Emis
3g 3D spectrum 3D
3h average report AvRep
3i ATR spectrum ATR
3j arithmetical result, transmittance AriTR
4a arithmetical result, absorbance AriAB

4b absorption spectrum AB
4c trace Trace
4d first derivative 1.Der
4e second derivative 2.Der
4f subtraction report Subtract
4g molecular structure Strc
4h search result Search
4i unknown spectra type Spec
4j single channel spectrum, sample ScSm

5a annotation ANNO
5b Cluster Analysis Clus
5c signature Sign
Furthermore, modifications of the above icons exist. For example, R represents

the real part and I the imaginary part of a complex datafile. A data block accen-
tuated with a shadow indicates a 3D data block.
Icons Used For OPUS Commands
Listed are the tool bar icons of most common OPUS commands.
New workspace Draw ellipse

Open Draw line
Close workspace Draw rectangel
Send workspace Insert table
Cut Move
Copy New page
Paste Delete page
New spectrum window Delete
New report window Clear frame
New 3D window Page properties
Tile Object properties
Cascade Lock
Quick print Back (frequency range)
Print Forward (frequency range)
About OPUS Scale all
Scale y
Stacked
Page back
Page forward

Baseline correction Integration
Spectrum subtraction Quantitative analysis 1
AB <–> TR conversion Set up Quant 1 method
Straight line generation Signal -to-Noise ratio
Spectrum calculator Peak picking
Cut Quick identity test
Normalization Conformity test
Make compatible Spektum search
Convert spectra Peak search
Smooth Information search
Derivative Structure search
Frequency calibration Initialize library
Raman correction Store spectrum in library
Black body Library editor
Interferogram to spectrum conversion Library browser
Inverse FT Quantitative analysis 2
Post zerofilling Quant 2 analysis / file list
Fourier self-deconvolution Set up Quant 2 method
Symmetric FT Identity test
Kramers-Kronig Transformation Set up Identity test method
Extrapolation Cluster analysis
1/cm <–> µm Carbon Oxygen Analysis
Averaging 2D Correlation
Merging spectra ranges DMA

Measurement Edit parameters
Repeated Measurement Information input
Rapid Scan TRS Set up Info mask
Direct command entry Structure import
Optic setup and Service Edit / create structure
Optics diagnostic Attach structure
Temperature control Instrument test
Motorised stage control Load file
Video assisted measurements Unload file
Time resolved step scan Undo changes
Chromatography Save file
Step scan modulation Save file as
Data extraction Send file
Add traces Send file to GRAMS
Assemble GC file Send file to InStep
Assemble Map file Delete data blocks
Print spectra External program
Setup JCAMP/OPUS conversion VisualBasic Script
Macro converter Load data point table
Run macro Scan OPUS files
Debug macro Find OPUS files
Macro editor Clone entry
Compile macro Clone original
Additional Information
OPUS Macro Language

To learn more about the OPUS macro language refer to the “OPUS Program-
ming” manual.
Evaluate Menu – Additional Options

According to the needs of your experimental task you have the option of adding
extra modules’ for data evaluation to the Evaluate pull-down menu. Depending
on the complexity of the module, separate manuals exist to describe the mod-
ules commands and functions in further detail.

List of File Name Extensions
In the following, the extensions OPUS uses for file names are listed. This list
should only be regarded as complete for when this manual was printed. Addi-
tional extensions will be added in the future, as more options of OPUS are
developed. Extensions used for OPUS-OS/2 are only listed if they are also used
for OPUS.
Extension Used Bya Description

.CLA X cluster analysis
.CLG N scan/find OPUS file
.CON X conformity test
.DAT N Pirouette file, used by InStep software
.DX X JCAMP file, also DX1, DX2...
.INT X integration method
.MAC O macro file
.MTB N macro file
.MTD X library method
.MTX N macro file
.NTI N optical bench configuration file
.OWS N OPUS workspace
.PCT X parameter correlation table used for JCAMP-DX
.PLE N printing template
.PLT O printing template
.Q1 X QUANT 1 method
.Q2 X QUANT 2 method
.RED N OPUS help file
.S01 X spectrum library, also S02, S03...
.SPC N GALACTIC spectrum library
.TXD X information mask
.XPM X experiment file
.TRS N TRS Experiment
.QT N Quality Test
.0 X OPUS file (any numerical extension)
a. O: used by OPUS-OS/2 N: used by OPUS X: used by both programs

Index Clear background 74
Clone entry 10, 31
Clone original 10, 31
CO2 bands 101
A Complex spectra 147
Abort task 68 Copy 13
Absolute peak position 63 All 13
Absorbance spectrum 102, 195 Correlation mode 72
Acquisition mode 71 Crosshair 12
Parameters 68 Cut 111
ADC 70, 144
D
Count 77
Add 13 Data block 9, 28
Comment 31 Data point table 26, 28
Freq. calib. 136 Default printer 219
Add selected 271 Delay time 70
Administrator 273 Derivative
Advanced measurement 66, 80 Savitzky-Golay 134
Advanced settings 68 Derivative 134, 196, 203
Aperture 69 Detector 61, 69, 146
Motor 65 Motor 65
Apodization 143, 151 Diagnostic functions 64
AQP 57, 84, 279 Dialog boxes 5
Reboot 279 Dielectric constant 153
Assign 231 Direct command entry 89
Atmospheric compensation 117 Display menu 217
ATR spectrum 116 Display settings 13, 272
Attach structure 45 Drag & drop 5
Auto align 77
Average report 162 E
Averaging 162 Edit menu 37
Axis 73, 247 Edit parameter 37
Edit/Create Structure 44
B New structure file 44
Background single channel 67 Scaling factor 45
Baseline correction 100 Evaluate menu 165
Scattering correction 102 Experiment file 69
Start interactive mode 100 External program 28
Black body correction 139 Extrapolation 155
Browser 8, 49
F
C File
Calibration 254 Create new info block 41
Calibration filter motor 65 E–mail 27
Change 13 Experiment 69
Color 13 Export 27, 63
Channel 69 Format 25
Channel motor 65 Import 28
Check signal 63, 82 Load 6
Name incrementation 273 Transformation 142
PDF 277 Internal background 124
Save 24 Interpolation 114, 159, 196
Send 27
Unload 24 J
File menu 23 JCAMP/OPUS conversion 258
File selection page 7
Filters 70 K
Find OPUS files 28, 30
Find in database 30 Kramers–Kronig transformation 153
Load selected files 30 Kubelka–Munk spectrum 115
Update database now 30 L
Fine auto align 77
Flaps motor 65 Language 277
Fourier Self-deconvolution 150 Large buttons 269
Fourier Transformation 73, 152 Laser 64
Frequency 70 Excitation frequency 80
Inverse 147 Power 82
Symmetric 147 Shut down 80
Frequency calibration 135 Wavelength 63, 248
Limits 17 Library 39, 213, 268
Limit resolution 144
G Line width 150
GRAMS 27, 63 Line-broadening function 150
L–limits 194
H Load Background 74
Spectrum
H2O/CO2 Compensation 119 Parameters 7
Help 277 Low folding limit 142
High folding limit 142 Low pass filter 71
High pass filter 71
M
I
Macro 89, 243
Icon size 269 Debugging 244
Icons 48, 55 Editing 244
Information block 40 Include in tool bar 245
Information input 39 Run a macro 244
Add information 40 Macro Conversion 244
New Text Mask 40 Make Compatible 113
Restore information 41 Reduce resolution 114
Text definition 40 Make Monotone 132
Mask 39, 41 Manipulate menu 99
InStep 28 Max. compression factor 159, 160
Instrument test 247 Measure menu 57
Insulators 155 Measurement 66
Integration 173 Acquisition mode 71
Integration data block 174 Acquisition parameters 70
Integration method 174, 175 Advanced settings 68
Interferogram 73, 151, 152, 247, 254 Aperture 69
Single sided 72, 143 Auto Align 77
Background 74 Open layout 240
Background signal gain 70 Optics diagnostic 90
Channel 69 Optics parameter 69
Correlation mode 72 Optics setup 57
Delay before measurement 70 AQP driver 58
Detector 69 AQP memory size 58
Display 73 AQP simulates an optic bench 58
Display single scans before measur AQP software 58
ment 73 Autoscroll 65
Double-sided interferogram 72 Devices/Option 59
Experiment file 67 Export Options 63
Fast return 72 Laser replaced 64
Fine auto align 77 Optical bench type 58
Forward/Backward 72 Repeat diagnostics test 64
Low pass filter 71 Reset laser dropouts 64
Optics parameter 69 Service 64
Parameters 68 Setup result spectrum 61
Preamplifier 69 Source replaced 64
Result spectrum 69 Update whole motor table 64
Sample signal gain 70
Save peak position 77 P
Scanner velocity 69 Page backward 218
Single-sided interferogram 72 Forward 218
Source 69 Peak picking 193
Stepper motor adjustment 77 sensitivity 193
Switch gain 70 Peak search 146
Window in points 70 Peak to Peak 191
Zerofilling 73 Phase
Menu configuration 270 Change 153
Molfile format 44 Correction 145, 147
Moving Mean 130 Resolution 73
Mult. for freq. calib. 136 Resolution 73, 142, 146
Spectrum 142
N
PLE
New 36 Displaying a spectrum 231
New layout 223, 240 Properties 232
New look 269 Spectral frame properties 233
New spectrum window 15 Table properties 237
New workspace 275 Text properties 240
Noise generation 129 Tool bar 225
Non–linearity correction 146 Workspace 225
Normalize 112 PLE browser 223
Min/Max - normalization 113 Plot Layout Editor 223
Offset correction 113 Polarizer motor 65
Vector normalization 113 Power spectrum 142
Number of scans 68 Preamplifier 69
Preserve integrals 159
O Preserve y–values 160
Open 36 Preview window 12
Principal file 113, 201 interferogram 87
Print 36, 219 Start loop 86
Information block 41 Use buffer 1 as background 87
Preview 36, 221, 241 Wait 86
Setup 36, 241 Wait input “High” 86
Spectra 220 Wait input “Low” 87
Template 219 Rapid scan time-resolved measurements 84
Printer Font 16 Reduce resolution 114
Properties 13 Reference spectrum 251
Pull–down menu 271 Reflectance spectrum 116, 153, 195
Refractive index 153
Q Registered window 51
Quant 1 178 Registration 267
Add component 179 Remove 13
Analysis 189 Repeated measurements 83
Calibration 178 Report 36
Calibration function 183 Report block 16
Calibration result 185 Report window 15, 51, 174
Calibration set 184 Resolution 63, 68, 70, 148, 150
Correlation coefficient 190 Result spectrum 61, 69
Define integration method 182 Root mean square 191
Difference vs. true 186 Routine measurement 66
Fit vs true 186 Rubber band 102
Remove selected spectra 181
S
Sigma 190
True vs. x 186 Sample changer motor 65
Quick Identity Test 200 Sample parameters 37
Sample single channel 67
R Save background 74
Raman correction 137 Save File As 24
Reference spectrum 138 Change path 24
Experiments 62 Data point table 25
Laser wavenumber 117 JCAMP 25
Laser wavenumber 117 Max. 64 KB 26
Measurement 80, 145 Mode 25
Spectrum 117 Overwrite 24
Rapid Scan Separator 26
Comment 86 Save peak position 67, 77
End loop 86 Save workspace as 276
Measure N scans 87 Savitzky–Golay algorithm 132, 134, 196
Measure NSS scans 87 Scale all 11, 218
Message box 86 Scale display 76, 218
Optic command 86 Scale Y 218
Reset time base 86 Scan OPUS Files 29
Set buffer 86 Scan time 68
Set output “High” 87 Scanner velocity 69
Set output “Low” 87 Scattering correction 102
Split double-sided interferogram 87 Search
Split forward/backward Add libraries 214
Algorithm 212 Status bar 49
Change list 214 Stepper motor 64, 77
Check library 214 Stop Task 68
Library 213 Straight line generation 109
Minimum hit quality 212 Straylight Correction 123
Parameter 211 Structure Import 43
Remove libraries 214 Subtracting spectra 103
Report 215 Subtraction data block 106
Select library 213 Switch gain 70
Sensitivity 212
Use existing peak table 212 T
Semiconductors 155 Temperature control 91
Sensitivity 212 Clear 91
Setup Info Mask 41 Extended commands 91
Clear all 42 Read temperature 91
Next page 43 Save settings 91
Restore original 43 Serial port default settings for this
Save definition 43 device 91
Setup menu 257 Set temperature 91
Shift 12 Wait for temperature 91
Shortcuts 5, 278 Time-resolved measurements 84
Show all 12 Tool bar 20, 47, 225, 245
Show all functions 270 Commands 48
Show Report 40 Customize 47
Signal gain 70 New 47
Signal-to-Noise ratio 72, 151, 191, 247, 254 Tool bar configuration 268
Fit parabola 191 Tooltip 269
Single channel spectrum 116 Transmittance spectrum 102, 108, 195
Smooth 132, 134, 196, 203
Savitzky-Golay 132 U
Source 64, 69, 247, 254
Source motor 65 Undo Changes 24
Spectrometer model 58 User rights 271
Spectrum block 142 User settings 272
Calculator 109 V
Spectrum conversion 107, 115
Absorbance spectra 116 Validation menu 247
ATR 116 Vector normalization 202
Kubelka-Munk 115 View menu 47
Logarithm 116 VisualBasic scripts 28
Raman spectrum 117
Single channel spectra 116 W
Spectrum search 210 Warning sign 78
Spectrum subtraction 104 Window
Spectrum window 11 3D 17
Axes 38 Allow Docking 55
Display 217 Cascade 53, 217
Display Limits 13 Float in main window 55
New 51 Hide 55
Properties 13 Lock 12
Resize 12
Spectrum 11
Tile 53
Zoom 217
Window menu 51
Workspace 36, 275
X
X-axis 158, 218, 247
Y
Y-axis 247
Y–Limits 197
Z
Zerofilling 73, 143, 148
Zoom 12, 218

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Spectroscopic Software

Figure 1: Windows Start Menu

Bruker Optik GmbH OPUS Reference Manual 1

Figure 2: OPUS Login Dialog

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Figure 3: About OPUS Dialog

Click on OK to open the OPUS user interface. The interface appearance

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Figure 4: OPUS User Interface

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Figure 5: Example of a Dialog Box with Two Tabs

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2.1 Loading and Selecting a File

Load Spectrum Dialog Box

• use the Load File command from the File menu,

(a) (b) (c) (d) (e) (f) (g)

(h) (i) (j) (k)

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j) It is also possible to load spectra of different formats, e.g. JCAMP-DX or GRAMS.SPC

Select Files Option

Figure 7: Example of Select Files Option

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Figure 8: Convert Spectra – Parameter Mismatch

2.2 OPUS Browser Window

(a) (b) (c)

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If you select one file using the left

Additionally selected by using

Figure 10: Select files

If you right click on a file name, a pop-up menu opens.

Figure 11: Pop-Up Menu for File Manipulation

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File has been

Figure 12: Pop-Up Menu for Spectrum Manipulation

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2.3 Spectrum Window

Lock Window Size

Figure 13: Spectrum and Overview Window Showing Lock Button

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Figure 14: Pop-up Menu within the Spectrum Window

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Properties opens the Display Settings dialog box.

Figure 15: Display Settings – Display Limits

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Figure 16: Display Settings – Axes

Figure 17: Display Settings – General

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2.4 Report Window

Figure 18: Report Window

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The information included in the report block is displayed in form of a directory

Figure 19: Report Window - View Properties

2.5 Datafile History

A special type of report window is Datafile History. Any manipulation made in

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History Datafile history History list

Figure 20: Report Window Showing the Datafile History

2.7 Selecting Frequency Limits

• Select the frequency range interactively.

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Figure 21: Frequency Range Selection

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