README ProMOL assist in visualization and identification of small catalytic sites. ProMOL (C) Copyright 2004-2010 Charlie Westin, Brett Hanson & Paul Craig GPL, No Warranty 4.1 Release Candidate 2 by Mario Rosa 7 December 2010 Special Thanks to the following for their contributions to ProMOL: Laura Grell, Chris Parkin, T.J. Esposito, C. Wischmeyer /*************************** GPL NOTICES ****************************** * * * This program is free software; you can redistribute it and/or * * modify it under the terms of the GNU General Public License as * * published by the Free Software Foundation; either version 2 of * * the License, or (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program; if not, write to the Free Software * * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA * * 02111-1307 USA * * * **********************************************************************/ ProMOL is a product of the Structural Biology Extensible Visualization Language (SBEVSL) project, supported in part by Award Number R15GM078077 from the National Institute Of General Medical Sciences. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute Of General Medical Sciences or the National Institutes of Health. The purpose of ProMOL is to assist in the visualization of protein structures in PyMOL. As well as assist in the identification of small catalytic site, and creation of catalytic site motifs. ========================================================================= ProMOL Installation Instructions ProMOL is a plugin for PyMOL. PyMOL is available as an open source program from http://sourceforge.net/projects/pymol/ and is incorpoated into many unix releases. PyMOL is also available in proprietary versions from http://www.pymol.org. See that website for information on PyMOL licensing. PyMOL is a program that was written by the late Warren DeLano. PyMOL is a trademark of Schrodinger, LLC. ProMOL is a plugin for PyMOL, not a derivative part of PyMOL, but depends on having a copy of PyMOL in order to operate. Therefore, in order to use ProMOL, you first must have a copy of PyMOL installed. Download PyMOL from http://pymol.sourceforge.net and install to default location. ProMOL can be downloaded in a compressed file format from http://sourceforge.net/projects/sbevsl/files You can choose to download either a .tar.gz compressed file (ProMOL-4.1rc2.tar.gz as of July 13, 2010) or a zip compressed file (ProMOL-4.1rc2.zip as of July 13, 2010). The way you expand the file depends on your operating system. In unix or linux systems, or using MINGW under windows you may unpack the tarball with gunzip < ProMOL-4.1rc2.tar.gz | tar xvf - Windows and Macintosh systems may have a native application that will expand your .tar.gz or .zip files; if not you may wish to consider using Stuffit Expander or WinZip. If you have not already done so, first install PyMOL. Under Macintosh OSX you may need to rename the MacPymol application to MacPymolX11Hybrid, in order to get access to plugins. To install ProMol.py, copy ProMol.py and the folder ProMol into the correct place in the directory tree used by PyMOL for plugins. For example, for PyMOL 0.99 under MS windows: C:\Program Files\DeLano Scientific\pymol\modules\pmg_tk\startup\ On other systems you will need to find the portion of the pymol installation tree that contains modules/pmg_tk/startup and place ProMol.py and the folder ProMol in the startup folder. For example in a fink PyMOL installation for python 2.4, 2.5 or 2.6 under Macintosh OSX, the ProMol.py file and ProMol folder belongs under /sw/lib/pymol-py24/modules/pmg_tk/startup or /sw/lib/pymol-py25/modules/pmg_tk/startup or /sw/lib/pymol-py26/modules/pmg_tk/startup When all files are in place, the ProMOL interface can be run by choosing ProMOL from the PyMOL plug-in menu. ========================================================================= Work done in part with support from NIH and Nation Institute of General Medical Sciences (NIGMS) under Grant number 1R15GM078077-01. ASBMB Annual Meeting April 28 -- May 3, 2007 Washington, DC Using PyMOL's Selection Algebra for Enzyme Catalytic Site Prediction B. R. Hanson, C. Westin, P. A Craig <> American Crystallographic Association Meeting 21 -- 26 July 2007 Salt Lake City, Utah ProMOL, Simplification and Increased Functionality of PyMOL B. Hanson, C. Westin, L. Slatest, P. Craig <> American Crystallographic Association Meeting 31 May -- 5 June 2008 Knoxville, TN Homology Exploration with ProMOL C. Wischmeyer, P. Craig, H. Bernstein The ProMOL plugin for PyMOL is an intuitive user interface that gives users access to many of the complex tools that exist within PyMOL, without requiring that the user learn to program in Python. Among its many tools, ProMOL features a motif­matching interface that can compare enzyme active sites based on the relative positions of the catalytic residues. Tools found in ProMOL can be used to compare any structure with more than 30 known calalytic active site motifs, which were drawn from the Catalytic Site Atlas (http://www.ebi.ac.uk/thornton­srv/databases/CSA/). The motif analysis tool can be fine tuned to narrow or expand the three dimensional search space for active site alignment. Alignment results for enzyme classes across different taxonomic categories will be presented and compared, along with suggestions for implementing more effective alignment strategies with the motif tool in ProMOL. ========================================================================= ChangeLog: Revision 119 Modified Tue Dec 7 by vinnyrose Version 4.1rc2. Minor backwards compatibility fix. Updated readme. Revision 115 Modified Thu Aug 5 by vinnyrose Version 4.1rc1. Added and alignment option in the motif finder. [Turn alignment on and double click on a motif in the result box to see the alignment of the template pdb to the test pdb. The color of each may be specified by clicking on the color boxes adjacent to "template color" and "motif color". These boxes are only clickable if alignment is clicked on. The alignment box does not have to be clicked on prior to starting a test, but it does need to be clicked on prior to double clicking a result if you want the alignment to appear. You cannot align a PDB with itself.] Many sorts have been changed to be faster and to have backwards and forwards compatibility. All motifs have been changed to include a LOCI attribute which includes information on where the residues were located in the original template pdb. The motif maker has been updated to include the LOCI attribute. The color functions have been changed to make the custom colors more optimized and to avoid conflicting colors. global.show_as function added to compensate for cmd.as being changed to cmd.show_as due to reservation of 'as' in python 2.6. More reliable and faster finding of chains in global.update function. Revision 110 Modified Tue Jul 20 by vinnyrose Fetch falls back to non-compressed on zlib error. Thanks button removed. Revision 109 Modified Wed Jul 14 by yaya-hjb Add actual authors on copyright line. Add gpl.txt Needs a readme. -- HJB Revision 107 Modified Tue Jul 13 by vinnyrose System dependent bug fix. Revision 105 Modified Tue Jul 13 by vinnyrose ProMol Changed persistent storage. Changed gui dictionary to a class object. Several small bug fixes. Promol will now advise the user to install the 'ProMol' folder if it was not installed in the startup folder. Bug in random pdb fixed, now it actually is random. Version 4.0rc4. ConSCRIPT Some small fixes. 2.0rc4.1 Revision 98 Modified Tue Jul 6 by yaya-hjb Raise rc number to 3.2 -- HJB Revision 94 Modified Tue Jun 29 by vinnyrose ConSCRIPT select function fixed. Many changes made to the structure of the code including making the class truly classified. Before all the functions were in the init of the class. The handle command now looks at token equality instead of command substrings. Parsing colors has been modified to a smaller code base. Promol: some small bug fixes in the motif maker that occur when unwanted spaces occur in the input fields, a fixed motif was added. A better way of updating motif files is needed when this is all distributed. Version changed to 3.6.2. Version 4.0 candidate 3.2 Revision 93 Modified Fri Jun 25 by vinnyrose Some small bug fixes. Version changed to 3.6.1. Version 4.0 candidate 3.1. Revision 92 Modified Tue Jun 22 by vinnyrose Some small bug fixes. Updated the motif finder to support batch processing. Motif maker has the capablity to change the order of the motifs being made. Several organizational changes such as folder names and locations. ChimeConverter is now active, and accessible with the 'c' command prefix. Pmw has been replace by tkinter functions in many places. Version changed to 3.06. Version 4.0 candidate 3. Revision 88 Modified Fri Jun 11 by vinnyrose Added all the motifs made so far. Created error reporting on motif loading. Changed welcome screen. All pdb's entered into motif maker will be lowercased. 4.0 release candidate 2. (3.05) Revision 87 Modified Thu Jun 10 by vinnyrose Several changes. The motif maker has some bug fixes, as well as the ability to check against homologs and random pdb's. The motif finder uses a levenshtein distance calculation and reports the minimum and maximum (min/max) edit distance found, if the min and max are the same it reports one distance. It searches into each chain individually and the whole structure. In addition it searches through every permutation of residues in cases where that is applicable. Version changed to 3.04. Version 4.0 candidate. Revision 86 Modified Mon Mar 22 by vinnyrose Residues are capital insensitive in motif maker, multiple ec numbers can be entered separated by a comma. The motifs are going through the last steps to transfer them to individual files. Revision 85 Modified Sun Mar 21 by vinnyrose Some small changes, and preparing the motifs to be separated into individual files Revision 83 Modified Wed Mar 17 by vinnyrose More changes to the motif maker. Revision 82 Modified Wed Mar 17 by vinnyrose Changes to ConSCRIPT to make it compatible with Linux. Many changes to ProMol. Changed motif maker to have it's own tab, and am still working on making it compatible with motif finder. Made changes to make it more compatible with linux and need to make more changes in that area. Changed the GUI in many areas. Deleted many motifs that don't seem to have a use right now. Revision 81 Modified Tue Feb 16 by vinnyrose Remove reference to batch motif. Revision 74 Modified Wed Feb 3 by vinnyrose Temporarily commented out some tabs. Revision 73 Modified Mon Feb 1 by vinnyrose Moved remote_pdb_load into the Promol_dir as well as make a few changes in the code. Made the motif finder faster. Revision 65 Modified Tue Jan 26 by vinnyrose Jess templates are done. Motif finder reworked. Random PDB finder is working again. Revision 63 Modified Thu Jan 7 by vinnyrose Hooking stuff onto the new organization. Most Motif related functions have been hooked on. Revision 62 Modified Thu Dec 24 by vinnyrose Made lots of organizational changes. Stable but with many bugs. Revision 60 Modified Tue Dec 15 by vinnyrose Made changes to the built-in motifs. No functionality changes, just making things prettier. Still unstable, latest stable in 57. Revision 59 Modified Mon Dec 14 by vinnyrose This revision is absolutely positively unstable, DO NOT USE IT! Removed unnecessary files and folders. Removed ProMOL_302. If you want the latest stable go to revision 57. Changed amino acid pictures names so that they are not confusing. Changes to ProMol.py include: separating the code into multiple files Optimizing the code standardizing the formatting This is the first commit in several to come that will dramatically change the code. The functionality in most cases will not be changed. Much of the indentation is not correct due an attempt to standardize. Indentations will be fixed in a future revision. Revision 58 Modified Mon Dec 14 by vinnyrose ~/Desktop/commit.rtf Revision 57 Modified Thu Jul 9 by vinnyrose the make motif function can now handle between 2 and 10 residue motifs and is much faster. The make motif window can now handle empty rows. Amino acid list are in alphabetical order. Trimmed white space at the end of lines. Made global list of amino acids three letter codes. And made global list of alphabetical letters. Revision 55 Modified Fri Jun 12 by vinnyrose Revisions made to makemotif fuction: This revision is able to build a motif for active sites that have repeating amino acids. The code has been commented so that it can be followed more easily and the motifs that are built now have a smaller file size. The while loops were improved and variable names were changed. -MROSA Revision 40 Modified Tue Jul 22 by yaya-hjb Correct spacing garbled on last upload -- HJB Revision 39 Modified Wed Jul 16 by yaya-hjb This update allows users to use commands that were once only available in ProMOL in the command line as well as scripts (as long as ProMOL itself is open). See ProMOL_README.txt. Mod by C. Wischmeyer. -- HJB Revision 36 Modified Wed Jun 25 by yaya-hjb Mods by Corey Wischmeyer introducing commands for ProMol ops See the sbevsl wiki on sourceforge for details. Revision 34 Added Wed Jun 11 by yaya-hjb Copied from: trunk/promol/ProMOL_302.py revision 33 Remove version from name of ProMol.py, update to 303 with batch motifier. Mods by Corey Wischmeyer. -- HJB