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This is version 4.1.0 NEWS FOR VERSION 4.1.

0 ==================================================== - Added new tools to process surfaces, and rearranged the Tool menu accordingly. - possibility to detect hydrophobic patches - detection of grooves (open cavities) - Added an atom radius table in the usrstuff directory. If present, the table is read at startup. Tis can be modified override the default size of the spheres drawn on screen for a given atom type. - updated some dialogs for the Mac version to support copy/paste. - fixed a bug where negative residue numbers were saved with an incorrect residu e number. - fixed a bug that prevented some hydrogens to be loaded (more specifically those whose name was similar to HG12, for example. - fixed a bug that caused a crash when long path/filenames were used, for example when Pov-ray scenes where saved in deeply nested directories. - fixed a bug that prevented to copy the graphic content of the rendering window . - fixed the color refresh issue when atom color preferences are altered. - honor the "update threading display" flag (automatically recomputing the threading energy when the alignment is modified). - Abandon of the default non openGL rendering mode. This was causing various color issues on some Apple computers, since it required a screen set to thousands of colors. On some models, Apple supports only million of color devices. Keeping this custom "fast" rendering mode does not make sense anymore given that nowadays all computers ship with hardware accelerated openGL cards. known bugs: - Solid Ribbons can look bad on some graphic cards / drivers, for example AMD Ra deon HD6850M I have not experienced this issue myself, and hence it is difficult for me to fix it. - Some PC users have reported an issue with an intenpestive switching to stereo mode when they are clicking on atoms or performing measurements. Again, I have never experienced this issue myself, and cannot fix it. NEWS FOR VERSION 4.0.4 ==================================================== - Updated the Blast against Uniprot function. NEWS FOR VERSION 4.0.3 ==================================================== - Measuring a distance already measured will clear it. - Improved 3D motifs generation.

NEWS FOR VERSION 4.0.2 ==================================================== Bugs fixed: - The Select AAkind menu is now working correctly. - Improved the motif searching capabilities. - Fixed the URL used to import Uniprot sequences from the import menu. NEWS FOR VERSION 4.0.1 ==================================================== Bugs fixed: - The C6 atom of Thymine is now correctly loaded. - Fixed the POV-Ray output endless loop on the PC version. - The occasional crash while saving PDB files (such as 2i37) on the PC has been fixed. - Updated the address of the Uppsala Electron Density Map Server. NEWS FOR VERSION 4.0 ==================================================== - First of all, and most importantly, PC and Mac versions have been resynchroniz ed. It means that the same features are available on both platforms. - This version supports direct login and modelling submissions to the SwissModel Workspace as well as retrieval of projects and template identification from the workspac e. Thanks to Prof. Torsten Schwede and Konstantin Arnold for adapting the workspa ce to allow for direct communication! - The import menu has been enhanced and can be used to import results of past mo delling requests, sequences from both UNIPROT and NCBI, nucleotide sequences, electron density m aps and compounds. - The NCBI taxonomy is supported. - Saved files retain most of the PDB header information. - The interface provides new alignment functions, in particular the possibility to realign a section of an alignment using an external server running MUSCLE. - Using two "guiding" sequences, it is now possible to merge two preexisting ali gnments. This is particularly useful to merge a sequence alignment with a structural al ignment. - It is now possible to mutate nucleotides (DNA). - It is possible to Save/Restore selections. - There is a better support for copy/paste operations: - It is possible to copy the rendered image into the clipboard - It is possible to paste a raw sequence into the workspace. - It is possible to copy sections of model and paste coordinates (all, backbo ne or sidechain) onto an other layer. - Vertical Scrollbars have been added to the LayerInfo and Alignment Window. - Brought Help files up-to-date with current version (see Help Menu). - Better integration with the SWISSMODEL workspace: possibility to submit and re trieve projects directly from the interface.

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Possibility to search a selected subset of PDB for 3D motifs. Fixed several stability issues on Intel Macs. Added a script directory, that allows to quickly access new functions added vi external scripts. I also would like to thank Prof. van Aalten and Alexander Schuettelkopf for th possibility to use there PRODRG server to obtain 3D coordinated from the 2D compounds downloa ded from Pubchem. - Finally, I like to point out that once again Prof. Gale Rhodes is testing the new version and updating his tutorial to fit the new functionalities. He has been using and te sting Swiss-PdbViewer since its first release in early 1995! NEWS FOR VERSION 3.9b2 (Mac) ==================================================== It seems that a lot of macintosh users had been using the latest OS9 version und er classic for their work. Unfortunately, with the transition to the intel based platform, classic is no longer supported. Therefore, it became urgent to produc e a version that would run natively on the new hardware. I spent some time fixin g the numerous problems present in the native OSX alpha version, and, at the sam e time produced a universal binary. This version has a few features that are not yet documented in either the manual or Gale Rhodes' tutorial (mostly differences in the Layers info and alignment w indows behaviors see below). Although those features are not fully polished, giv en the number of requests for the native OSX version and the start of the new ac ademic year, I felt it was more important to release a usable OSX universal beta version now than to wait for a polished version. So please remember it is a bet a. - The Magic Fit problem affecting OSX Intel-based machines was actually not fixe d. Apparently it was only working in the debug version but not when compiled wit h optimizations turned on. I upgraded my compiler and it is now working well. Thanks to Gale for testing th e version. - Several display glitches when openGL solid rendering was turned on have been f ixed. - Depth cuing is now turned on when the slab is enabled (Display Menu) during 3D rendering, which makes it easier to perceive perspective. The depth cuing will start at the centered atom and beyond. Therefore, everything which is in front o f centered atom is bright, whereas everything which is behind it will be progres sively darker. As always, moving the mouse left or right while the Shift key is held down will narrow/enlarge the slab section. Moving the mouse up or down will push/pull the visible slab away/toward the viewpoint. - The Export image function when solid rendering is enabled is fixed. VERSION 3.9b1 KEY DIFFERENCES WITH PREVIOUS VERSIONS ==================================================== - The default button of the import dialog (ie hitting return after having typed a name) will now connect to the remove spdbv server to fetch files instead of th e local disk. - Support for two mouse button has been enabled: It is still possible to use tab to cycle among tools and use only the left but ton, but otherwise, if the rotation tool is selected then:

left button = rotation right button = move left + right = zoom. which corresponds to the PC version. - It is now possible to move and rotate the view during the seleciton of atoms - When one of the picking tool is enabled, the name and coordinates of the atom the mouse is over will be displayed in real time in the toolbar, which is useful to ensure that the correct atom is picked. - The control panel now contains a new column 'sel' which determine which layers will be affected when (most) commands are invoked while the SHIFT key is held d own. - It is possible to load gapped fasta files (from amino-acids or nucleotides) us ing the Swissmodel menu (or by drag and drop) - Checkboxes in the alignment window preferences will allow showing secondary st ructure and/or nucleotides in addition to the protein sequences. - When the graphic window is active, using the edit:copy function will copy the image to the clipboard and thus can be pasted in other applications - When the alignment window (or control panel) are active, the edit:copy functio n will copy the one letter code amino-acid sequence of selected residues of the current active layer to the clipboard - Likewise, when the alignment window is active, the edit:paste command will pas te the content of the clipboard as a protein sequence which will appear as a new layer. - In the alignment window, it is now possible to copy/paste selections across la yers. This will essentially replace the selected target residues (coordinates, k ind etc...) with source ones.