AntigenMap 3D Manual

Systems Biology Laboratory

Dept. of Basic Sciences

CVM-MSU

February 3, 2012
Contents
1 Quick Start 2
1.1 Loading Data . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 Using the 3D Map . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 The Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

2 Input Format 8

3 Example Usage 8
3.1 View a group(s) of antigens . . . . . . . . . . . . . . . . . . . 8
3.2 Measure distance between two antigens . . . . . . . . . . . . . 8
3.3 Export a screenshot . . . . . . . . . . . . . . . . . . . . . . . . 9

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1 Quick Start
AntigenMap 3D is a three dimensional antigenic cartography tool with many
built in analysis tools. This section will give a quick introduction on how to
use AntigenMap 3D and an overview of the major features. Figure 1 shows
an example of the AntigenMap 3D interface.

Figure 1: The AntigenMap 3D web interface

1.1 Loading Data

1. Figure 2 shows the start of any AntigenMap 3D run; fill in the form as
shown in Figure 3 and click submit.

2. After processing antigen coloring is possible, Figure ?? shows the start

2
 Figure 2: The starting form

of color selection. Use the color picker to select colors for antigen
groups. Click the submit button to proceed to the 3D map.

3. The java applet will ask permission to run Figure 5, click run to con-
tinue loading the map. Figure 6 shows a loaded 3D antigen map that
a user can view and manipulate or save for later use.

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 Figure 3: The filled in form

Figure 4: The color selection form

1.2 Using the 3D Map

4
 Figure 5: The Java Applet security window

Figure 6: The AntigenMap 3D web interface

Basic navigation

• Left-click and drag to rotate the map

• Use the scroll wheel or SHIFT drag the mouse to zoom

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1.3 The Menu
The Menu — Right click to open the menu
• Select — shows the number of currently selected antigens

– Display Selected — toggles display of unselected antigens

– All — Selects all antigens
– None — Clears all selections
– Invert Selection — selects the currently unselected antigens and
unselects the currently selected ones

• Set Selection — Selection methods

– Off — disables click to select

– Set Center — Sets the center rotation point the the clicked antigen
– Label On/Off — Toggles display of labels for selected antigens
– Select Antigen — Sets selection of individual antigens by mouse
clicking
– Select Group — Sets selection to groups of antigens

• View — Default views ( default: front )

• Style — Adjusts the style of display

– Perspective Depth — Toggles drawing ”farther away” antigens

smaller
– Boundbox — Toggles display of the bounding box
– Axes — Toggles display of the X, Y, and Z axes
– Sterographic — Options for 3D displays
– Labels — Labeling options for antigens
∗ No Labels — Hides the display of labels for antigens
∗ With Antigen Name — Displays the names of antigens as
labels ( on by default )
– Axes — Display options for the axes
– Boundbox — Display options for the bounding box

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• Color — coloring options
– Labels — Color options for labels
– Antigens — Color options for antigens
∗ Make Opaque — Render antigens in solid colors
∗ Make Translucent — Render antigens in semi-transparent col-
ors
∗ by Antigen Group — Color antigens by group ( default )
∗ by Antigen Number — Color antigen uniquely
– Axes — Changes the color of the axes
– Boundbox — Changes the color of the bounding box
– Background — Changes the color of the background ( default:
black )
• Zoom — Zoom options
• Spin — Enables/Disables automatic spinning of the map
• Measurements — Options for measuring antigenic distance
– Show Measurements — Toggles display of measurements
– Click for Distance Measurements — Enable single clicking to mea-
sure between two antigens
– Clean Measurements — Remove all previous measurements
– List Measurements — Displays a list of all current measurements
• Save — Saving options
– File — Saves the 3D coordinates of the antigen map
– JPG Image — Saves the current view as a JPEG image
– PNG Image — Saves the current view as a PNG image
– POV-Ray Image — Exports the current view for rendering in
POV-Ray
• Language — Changes the language of the menu ( note some items may
not have translations )
• Console — Opens the Jmol console for advanced usage

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2 Input Format
The Input format is a tab delimited data format exportable from a spread-
sheet ( an example sheet is available online ). The first row of data lists the
number of antigens and the number of antisera. The second row contains the
column headers and the antisera names. The third row contains the reference
numbers used in normalization methods 4 and 5. The rest of the rows are
the antigen names and groups followed by their HI data.

Example:
num. antigens → num. antisera ←-
ID → Group → antisera1 → antisera2 ←-
Reference → 0 → 100 → 500 ←-
antigen1 → G1 → 20 → 200 ←-
antigen2 → G1 → 0 → 300 ←-
antigen3 → G2 → 625 → 30 ←-

3 Example Usage
3.1 View a group(s) of antigens
1. Menu → Select → None

2. Menu → Set Selection → Select Group

3. Left click on the group(s)

4. Menu → Select → Display Selected

3.2 Measure distance between two antigens

1. Menu → Measurements → Click for Distance Measurements

2. Left click on the two antigens

3. Repeat for all required measurements

4. Menu → Measurements → List Measurements

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3.3 Export a screenshot
1. Setup the window as you want the screenshot to appear

2. Menu → Save → JPG Image

3. Save dialogue opens for screenshot