ProMOL User Guide
Contents
1. a lt l edt 5 2 NT A y vi fp 0 EOSIN 1 i 1 DA X wank Cr Wey iV zi on Va 4 f y ah ae ie 4 Dt Figure 18 A The first image shows the default EZ Viz cartoon for a DNA protein complex PDB is 1d66 B The waters have been hidden EZ Viz Hide Water and on the View Options tab Cartoon Width has been reduced from 1 40 to 0 75 C the Cartoon Width has been returned to 1 40 while the Cartoon Thickness has been increased from 0 30 to 0 80 D The transparency for the protein part of the 1d66 has been changed from 0 0 to 0 50 without affecting the appearance of the DNA Users are encouraged to experiment with the View Options for use in demonstrations in class and also for use in publications Page 232. Figure 13 Measurements between atoms in active site residues in a serine protease The distances between various atoms on each residue displayed by PyMOL are used to create the three dimensional active site motif definition Calculations are based on the PDB entry 1AB9 gamma chymotrypsin Here is a step by step description of how to create a motif for 3a hydroxysteroid dehydrogenase type 3 based on pdb entry 1j96 Page 16 ProMOL Users Guide 7 25 11 O O O X ProMol Version 4 2 Release Candidate 2 Welcome EZ Viz Motif Finder Motif Maker iat Options Motif Maker PDB EC Precision Factor 2 00 1 Residue Chain Number BackBone Off 2 Residue Chain Number BackBone Off 3 Residue Chain Number BackBone Off 4 Residue Chain Number BackBone Off 5 Residue Chain Number BackBone Off 6 Residue Chain Number BackBone Off 7 Residue Chain Number BackBone off 8 Residue Chain Number BackBone Off 9 Residue Chain Number BackBone Off 10 Residue Chain Number BackBone off Export i Order Clear Test Save seen and Random Testing i Homolog C Random Test Open PDB Fetch PDB Random PDB Clear Help A Figure 14 The Motif Maker tab 3a hydroxysteroid dehydrogenase type 3 PDB id 1j96 is an annotated entry in the Catalytic Site Atlas CSA http www ebi ac uk thornton srv databas
3. ProMOL The compressed file is available for download in both zip and tar gz formats 1 Install PYMOL 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 and Linux releases PyMOL is also available in proprietary versions from http www pymolorg 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 Page 1 ProMOL Users Guide 7 25 11 2 Download PyMOL from http pymol sourceforge net and install to the default location on your system For installation of PYMOL on an MS Windows system ProMOL has been tested with PyMOL 0 99 1 0 1 1 1 3 and 1 4 see http molwiki org index php Windows Install For installation of PYMOL on a Mac under OS X ProMOL has been tested with PYMOL 0 99 1 0 1 1 1 3 and 1 4 see http molwiki org index php MAC Install For installation of PYMOL on a Linux system ProMOL has been tested with PyMOL 0 99 1 0 1 1 1 2 and 1 4 see http molwiki org index php Linux Install Download ProMOL ProMOL can be downloaded in a compressed file format from http sourceforge net projects sbevsl
4. Slatest L Craig P A EZ Viz a Tool for Simplifying Molecular Viewing in PyMOL Biochemistry and Molecular Biology Education 34 402 407 2006 Earlier versions of EZ Viz and ProMOL contained a very simplified PyMOL to Chime Rasmol Jmol command convertor This converter has been updated and enhanced dramatically with the ConScript plug in for PYMOL Mottarella S E Rosa M Bangura A Bernstein H J Craig P A ConSCRIPT Biochemistry and Molecular Biology Education 38 419 421 2010 The ConScript plug in and user manual can be obtained from http sourceforge net projects sbevsl X ProMol Version 4 2 Release Candidate 2 Welcome EZ Viz Motif Finder Motif Maker bi ia Options Preset Views Surfaces Cartoons By Residue Preset Movies Miscellaneous Electron Density Roving Roving Detail Automated Commands Select All Show Lines Color Red Update Selection Hide Lines Display Options Stereo Background Color Color Space Internal GUI Off Black PyMOL Show Open PDB Fetch PDB Random PDB Clear Help Ms Figure 2 The EZ Viz tab in ProMOL enables users to create interesting views and movies of their macromolecular structures using the drop down menus once a protein is loaded Users can then manipulate their structures without having to learn and use Python commands Page 8 ProMOL Users Guide 7 25 11 eo ey F X PDB Loa
5. enter the PDB code in the Homolog and Random Testing box on the Motif Maker window then click the test button in the same box Table 1 contains a list of structures tested and briefly summarizes the results The first 10 homologs listed in the CSA were tested then homologs found 10 20 and 40 positions later in the table were tested s PDB id Active Site Found Extraneous or Missing oo _ _ Pape es Asp ss Lys STAT None 1 _ fmmra_ Yes Aspa0 Tyrs Lys Histi7 Nome ee ee 1a80 No Asp45 Tyr50 Lys75 His108 It was found if the Precision Factor was increased to 2 3 labn No motif found The PDB file is alpha carbons only and won t work with ProMOL 6 tads__ Yes Yes Asp43 Tyrt6 Lys77 His110 Tyr48 Lys77 His110 7 dae4 Nooo No Alpha carbons only lafs Yes Asp50 Tyr55 Lys84 His117 No in both Chains A and B Yes Asp43 Tyr48 Lys77 His110 20 1el3 Yes Asp 43 Tyr48 Lys77 No His110 Page 20 ProMOL Users Guide 7 25 11 30 11wi Yes Asp50 Tyr55 Lys84 His117 No in both chains A and B Yes Asp50 Tyr55 Lys84 His117 Table 1 Homolog testing for the 1j96 motif 3a hydroxysteroid dehydrogenase type 3 When a new motif is built in Motif Maker it should be tested with 10 or more homologs of the structure The purpose of this testing is to look for true positives structures in which ProMOL clearly identifies the existing motif correctly Some may match perfectly other
6. image simply by selecting Water from the Hide menu in the Automated Commands area of EZ Viz Figure 5 The select show color and hide commands in this area are designed to enable users to manipulate the appearance of the structure without having to enter scripts Display Options support changing the status of the stereo mode background color color palette and the internal GUI for PyMOL which appears on the right hand side of the viewer window The internal GUI contains a list of selections within PyMOL information about the Mouse Mode in PyMOL and the control buttons for movies within PyMOL Page 9 ProMOL Users Guide 7 25 11 O O MacPyMOL fal protein A s E L icy dna A SIAL Gy rna A sH L icy hydrophobic A s E L ic hydrophilic Al SIA LL cl acidic A s EL c basic A s EL c ligands A s E L c Chain A A s EL c Chain B A s E L c Button Viewing Buttons Slab Residues TEN DEE E A E E O O MacPyMOL idna A irna AS hydrophobic A s L ic hydrophilic AAD acidic Als AY L c basic A sL Iic ligands Als IAL icy Chain A A s L ic Chain B A sE Lic sele Als IAL icy Button Viewing Buttons amp Keys Rota Move vZ Slab Box T 5 ral E Menu yenu PkAt Residues OL ER Oe WE Figure 5 The Cartoon version of 1qtq as implemented in EZ Viz after hiding the waters Page 10 ProMOL Users Guide 7 25 11 Motif Finder The Motif Finder tab gives the
7. the sections about the Motif Maker and Motif Finder tabs Clear removes all structures that are visible in the molecular viewing screen N N PDB Loader Please enter a 4 digit pdb code Cancel OK AOAN Invalid Code You entered an invalid pdb code Help is currently being re implemented and does not function at this time Page 6 ProMOL Users Guide 7 25 11 Welcome The Welcome tab is also the opening screen for ProMOL that identifies the plugin AOO ProMol Version 4 2 Release Candidate 2 Welcome EZ Viz Motif Finder Motif Maker View Options ProMOL Developed by the SBEVSL Project Licensed under GPL No Warranty Partial Funding Provided By NSF DUE 0402408 NIGMS 1R15GM078077 RIT and Dowling College This is ProMol 4 2 Release Candidate 2 User guide not included pending completion Open PDB Fetch PDB Random PDB Clear Help Mh Figure 1 The ProMOL welcome screen ProMOL is released under a Gnu Public License http www gnu org licenses gpl html The screen credits refer to funding from the National Institutes of General Medical Sciences a division of the National Institutes of Health and to the National Science Foundation Division for Undergraduate Education Page 7 ProMOL Users Guide 7 25 11 EZ Viz The EZ Viz tab includes most of the functionality from the EZ Viz plugin as described in the paper by Grell et al Grell L Parkin C
8. user access to the motif search tools in ProMOL Figure 6 The ProMOL code contains four sets of motifs based on three different approaches to catalytic site alignment 1 The JESS C C motifs are based on two atoms for each of the residues known to participate in a catalytic site based on the listings in the Catalytic Site Atlas http www ebi ac uk thornton srv databases CSA The JESS template files can be obtained from http www ebi ac uk thornton srv databases cgi bin CSS makeEbiHtml cgi file downloadTemplateLibrary html 2 The JESS functional atom motifs are based on the two atoms C and C as well as a third atom found in the side chain 3 The ProMOL motifs were built using the ProMOL Motif Maker found in the Motif Maker tab utilizing the same catalytic residues identified in the CSA The distances between each atom from each of the residues in a catalytic site were measured using PyMOL s built in measurement function These measured distances were used to create the three dimensional motif definition for that catalytic site 4 The UserMotifs are the ones that have been created by the user with ProMOL On the Mac they can be found in the folder Users username Library Application Support SBEVSL ProMol UserMotifs Windows AppData SBEVSL ProMol Unix sbevsl ProMol X ProMol Version 4 2 Release Candidate 2 View Motif Maker Options Welcome EZ Viz Motif Finder it Press Start to be
9. ProMOL Users Guide 7 25 11 ProMOL User Guide Development Team Eno Akpovwa Abdul Bangura Herbert J Bernstein Chantelle Brown Cyprian Corwin Paul A Craig Nikolay Darakev Greg Dodge Luticha Doucette Chanelle Francis Laura Grell Brett Hanson Katrina Henry Carly Keenan MaryEd Kenney Len Slatest Desiree Matthews Chris Parkin Mario Rosa Matt Rousseau Charlie Westin Funding Sources NSF DUE 0402408 NIGMS 1 R15 GM078077 01 and 3 R15 GM078077 01S1 Dowling College Rochester Institute of Technology Introduction ProMOL was created as a plug in to the molecular visualization program PyMOL found at http www pymol org The plug in ProMOL was implemented in Python and can be accessed from the plug in menu in PyMOL versions 0 99 1 0 1 1 1 2 and 1 4 after extraction to the appropriate directory It is supported for Windows XP Windows 7 Linux and Mac ProMOL also works with PyMOL version 1 3 in Windows XP Windows 7 and Mac OS X there are some problems with the Python library in Linux that interfere with ProMOL function in PyMOL 1 3 for Linux The source code for the ProMOL plug in and a PYMOL build containing the ProMOL plug in are freely available for download from http sourceforge net projects sbevsl files ProMOL Installation Windows Macintosh Linux and Unix The ProMOL plug in is available as a compressed file of a folder which contains the plug in file ProMOL py and a folder ProMOL which contains files used by
10. der Using EZ Viz Let s begin by opening a PDB file in PyMOL You can do this using the Fetch PDB button on the bottom of the Please enter a 4 digit pdb code ProMOL GUI You will need to enter the PDB ID for a structure of al interest in the popup window that appears and click on the OK p ok Cancel button For this manual we will use 1qtq glutaminyl tRNA synthetase complexed with tRNA and an amino acid analog When you do this the structure will appear in the PYMOL viewer window as a simple stick figure where each stick represents a bond between two atoms in the structure Figure 3 000 MacPyMOL St s te ics fat Ba ae protein A s I L ic dna AS HI ic rna A S EI L licy hydrophobic A s I L ic thydrophili S Lic acidic A s IL icy basic Als iA L icy ligands A s E L c Chain A A s A L c Chain B Als IAL icy Uy Rota Move Mov Slab Box Box C i Box Clip nps ovo PkAt Pki MvS2Z Sele Orig Clip Movd Cent Menu PKA TZ Figure 3 The appearance of 1qtq on loading in PyMOL You can change the appearance of this structure to generate a number of different views using the options in the Preset Views area on the EZ Viz tab For example if you select Cartoons from the Cartoon menu you then generate this view which shows the protein as a cartoon the DNA as a stick structure and the waters as spheres Figure 4 You can remove the waters from the
11. e by turning the backbone atoms on this simply adds the backbone atoms for the residues into the motif definition The motif definition can sometimes be improved by changing the order of the residues as they are entered in the Motif Maker box it is often advantageous to list the residues in the order of least common in a structure to most common in that same structure Once you are satisfied with a motif click on the Save button in the Motif Maker box and the motif will be saved to your computer the exact location depends on your operating system Page 19 ProMOL Users Guide 7 25 11 e Macintosh The motif definition file is saved as U_1j96_1_3_1_20 py to Users lt user name gt Library Application Support SBEVSL ProMol UserMotifs e Windows 2000 XP The motif definition file is saved as U_1j96_1_3_1_20 py to C Documents and Settings lt user name gt Application Data SBEVSL ProMol UserMotifs e Windows 7 The motif definition file is saved as U_1j96_1_3_1_20 py to C Users lt user name gt AppData Roaming SBEVSL ProMol UserMotifs e Linux The motif definition file is saved as U_1j96_1_3_1_20 py to sbevs ProMol UserMotifs The next step in designing a motif is to test it against homologs A list of homologs can be found on the Catalytic Site Atlas by clicking the Homologues of 1j96 link or the selected structure found under Other CSA Entries In the case of 1j96 more than 100 homologs are listed To test a homolog first
12. e query is shown in red and the result motif is shown in white B If desired the user can show cartoon by selecting show Cartoon from the S show menu next to all in the GUI oe Select a Color T Selection Red 255 fo g fffffc Page 14 Green 295 Rine 1252 ProMOL Users Guide 7 25 11 It is possible to change the colors used in the alignment by clicking on the colored square next to Structural Alignments either Template Color of Motif Color in the Show Alignment toolbox on the Motif Finder tab You can also click on individual residues in the PyMOL viewer window and the residue will be identified in the PyYMOL GUI For 1gtq you will receive this notice if you click on the beta carbon from Glutamate residue 34 You clicked 1qtq A GLU 34 CB Page 15 ProMOL Users Guide 7 25 11 Motif Maker The Motif Maker tab Figure 14 enables the user to build motifs based on definitions in the Catalytic Site Atlas Motif definitions in ProMOL are based on enzyme family representatives selected from the PDB and information from the CSA The distances between each atom from each of the residues in a catalytic site were measured using PyMOL s built in measurement function Figure 13 These measured distances were used to create the three dimensional motif definition for that catalytic site The motif definitions are then used to predict the presence of a catalytic site on the structure being tested
13. e template motif that you want to Page 13 ProMOL Users Guide 7 25 11 superimpose on the query motif P_1djq 1_5_8_2 in this case The result is shown in Figure 11 The alignment is not perfect but the three residues aspartate 267 histidine 172 and tyrosine 169 in 1djq aspartate 219 histidine 215 and tyrosine 211 in 1qtq are found in similar proximity in the two structures Note The result that bears the full name of the template motif P_1djq_1_5_8_2 in the image below can be ignored Use the two match_in selections match_in_1gtq and match_in_1djg in the image beow to manipulate the alignment MacPyMOL protein dna irna hydrophobic hydrophilic acidic basic eane Chain B al sIm iic P_idjq_1_5 8 2 ABR match_in_iqta ET dg ii OA OT match_in_1ldjq AJ s IEL iic Buttons amp Keys Rota Move Movz oa k Residues 17 1 A PyMOL gt _ lt m gt gt mis Y F MacPyMOL l all Show lata as protein Fines idna rna ribbon thydrophobic artoon hydrophilic ligands Chain B E ia s CAES EEEE _ ldjq a match_in_1djq 1 nic main chain sticks side chain i disulfides amp Keys Rota Move Mov d Slab re ae lax Clip Movs Sel si Cent Menu M enu k fa t Residues B Enea ICICI CIENA Figure 11 Alignment of Two Catalytic Site Motifs A The matching residues on the query protein and the selected motif are aligned Th
14. es cgi bin CSA CSA_Site_Wrapper pl Simply open the CSA in a browser enter 1j96 or the desired structure in the PDB code box and hit the Search button The page shown in Figure 15 should appear Page 17 ProMOL Users Guide 7 25 11 000 Catalytic Site Atlas aj http www ebi ac uk thornton srv databases cgi bin CSA CSA_Site_Wrapper pl mt Q7 Google Y uropean Bioinformatics Institute EBI Home About EBI Groups Services Databases Downloads Submissions Catalytic Site Atlas Version 2 2 12 d Annotated Site PDB code Swiss Prot code EC number Homologous Entry Oxidoreductase 3alpha hydroxysteroid dehydrogenase type 3 UniProt Swiss P52895 DBDI_HUMAN EC Class Prot Other CSA Homologues of 1 96 alta PDB entry 1 96 KEGG entry 1 3 1 20 Entries Entries for UniProt Swiss Prot P52895 PDBsum entry 1j96 Entries for EC 1 3 1 20 UniProt Swiss Prot P52895 IntEnz entry 1 3 1 20 templates exist for the 1mrq family 50 50 55 55 84 84 117 117 Figure 15 The Catalytic Site Atlas page for 1j96 To build a motif you ll need several pieces of information about a structure that you can find on the CSA page its PDB ID it EC and the residues that constitute its active site Figure 14 This information for 3a hydroxysteroid dehydrogenase type 3 was entered into the Motif Maker window as shown in Figure 16 Page 18 ProMOL Users Guide 7 25 11 HOO X ProMol Ver
15. files in the ProMOL folder It is important to note that clicking on the prominent green download arrow on this page or the main SBEVSL page on SourceForge net may lead you to another file that is part of the SBEVSL project You will need to open the ProMOL folder on http sourceforge net projects sbevsl files by clicking on the green triangle to the left of the ProMOL folder Similarly you should download the latest ProMOL version which will be the compressed file at the top of the file list You can choose to download either the zip or tar gz compressed file depending on your preferences and your operating system Unix or Linux 1 Expand the compressed file In unix or linux systems or using MINGW under Windows you may unpack the tarball with gunzip lt ProMol 4 2 tar gz tar xvf 2 Install ProMOL Plugins that consist of a single python file e g plugin py can be installed simply by using the Plugin gt Manage Plugins gt Install menu However this does not work with ProMOL because you need to install the ProMOL folder as well as the promol py file So you will need to take the following steps Page 2 ProMOL Users Guide 7 25 11 a Find the startup folder in your PyMOL installation For the default installation of PyMOL 1 2 under Ubuntu linux you can find the startup folder in usr lib pymodules python2 7 pmg_tk startup b Simply place the ProMol py and ProMOL folders inside the startup folder The next t
16. gin search Results double click to show Press Start to begin search Start _ PDB s to search comma separated f Tools Precision Factor 1 00 Show alignment Motif Color Query color Its Open PDB Fetch PDB Random PDB Clear Help MX Figure 6 The Motif Finder tab in ProMOL Page 11 ProMOL Users Guide 7 25 11 To use the Motif Finder a protein must be loaded into PyMOL You can do this by entering a PDB id in the box labeled PDBs to search If you would like to search more than one structure at a time just enter the PDB ids separated by commas Press Start to begin search Once the PDB IDs have been entered click the Start button to begin searching for motifs A popup window Figure 8 allows the user to choose which set of motifs he would like to search against For this manual a search of all motifs was performed but this takes a start while about 5 8 minutes per query structure against PDB s to search 200 motifs If you are focused only on 5 motifs you comma separated have created yourself the search is much quicker liov liow 8gch lqtq Once you have chosen your motif set the search begins On the search window Figure 7 the top bar indicates the search progress on the individual structure currently under evaluation and the bottom Figure 7 Entering the PDB IDs to search bar indicates overall progress for the full list of st
17. ime you launch PyMOL ProMOL should appear in your Plug ins menu c Ifyou have installed PyMOL to another location on your system you will need to copy ProMol py and the ProMOL folder to the location of the pymol installation tree that contains modules pmg_tk startup Once you have completed the installation launch PyMOL and look for ProMOL in the Plugin menu When all files are in place the ProMOL gui can be opened by selecting ProMOL from the plugin menu Windows 1 Expand the compressed file Windows 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 2 Install ProMOL Plugins that consist of a single python file e g plugin py can be installed simply by using the Plugin gt Manage Plugins gt Install menu However this does not work with ProMOL because you need to install the ProMOL folder as well as the promol py file So you will need to take the following steps a Find the startup folder in PyMOL In the default Windows installation of PYMOL 1 3 you can find the startup folder at c Program Files PyMOL PyMOL modules pmg_tk startup b Install ProMOL by copying ProMol py and the ProMOL folder to the startup folder If you have installed PyMOL to another location on your system you will need to find the portion of the PyMOL installation tree that contains modules pmg_tk startup Once you have completed the installation la
18. late structure have been found in the active site of the query structure 1qtq The second result is a comparison of 1qtq to itself so a Levenshtein distance Precision Factor 1 00 3 of 0 is expected There is also a Levenshtein distance of 0 from 1djq to v Show alignment 1qtq This is a bit of a surprise Motif Color considering that 1qtq is a glutaminy tRNA synthetase while 1djq is a Query Color o trimethylamine dehydrogenase e Motif group There are currently five motif groups in ProMOL o Jab means the motif is a member of the JESS C C group o Jfa means the motif isa member of the JESS functional atom group o Pab means the motif is a member of the ProMOL group that was designed with the PDB template used for the comparable Jab motif o Pfa means the motif is a member of the ProMOL group that was designed with the PDB template used for the comparable Jfa motif A designation of P means only that the Pab and Pfa motifs were identical as created by ProMOL o U means that this is a motif the user created using Motif Maker e Template file is the PDB ID for the structure that was used to build the template e EC is the Enzyme Commission number as reported by the Protein Data Bank We can compare the active sites for 1djq and 1qtq directly using the alignment tools found on the lower left hand corner of the Motif Finder tab Simply click the Show alignment check box Figure 10 then double click on th
19. ng up the option to Show Package Contents iii Traverse the tree to pymol modules pmg_tk startup b Copy ProMol py and the ProMOL folder to the startup folder If you installed PyMOL to some other location e g using fink or macports you will need to find the portion of the pymol installation tree that contains modules pmg_tk startup and place promol py and the ProMOL folder in the startup folder For example ina fink PyMOL installation for python 2 4 2 5 or 2 6 under Macintosh OSX the promol py file and the ProMOL folder belong 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 Note Any version of python below 2 6 may not be compatible with the latest ProMOL release 4 Once you have completed the installation launch PyMOL and look for ProMOL in the Plugin menu When all files are in place the ProMOL gui can be opened by selecting ProMOL from the plugin menu Special Notes for Installing ProMOL Under Mac OS X There are several alternate versions of PyMOL for use under Mac OS X In order to install ProMOL you need to use a version of PyMOL that accepts plugins In the example above a fink installation was assumed Alternatively you may wish to use a MacPorts install or to install MacPyMOL You will find instructions for all three at http pymolwiki org index php MAC_Install Page 4 ProMOL Users Guide 7 25 11 However it is impo
20. o possible to adjust the ambient light much as a photographer would adjust the lighting in an indoor studio to provide the best view A ProMol Version 4 2 Release Candidate 2 Welcome EZ Viz Motif Finder Motif Maker ieia Options Select yj Update Selection Reset Cartoon Cartoon Spheres Width ee Update size dii Update Thickness 0 30 Update Transparency 9 00 Update Transparency Update Sticks i 0 20 Tube Radius 0 50 Update Radius Update Automatic Transparency 9 00 Update Ambient Light Surface i i 0 25 0 00 Ambient Light Update Transparency Update Open PDB Fetch PDB Random PDB Clear Help A Figure 17 The View Options Tab in ProMOL can be used to adjust the default settings for cartoon sphere stick and surface values in addition to adjusting the ambient lighting One of two examples will be provided here users are encouraged to play with the options to see if the cartoon view can be made more interesting by for example changing the tube radius in the Cartoon box on the View Options tab Figure 18 shows the default cartoon generated from the EZ Viz tab for GAL4 a transcriptional factor from yeast that is bound to a 17 residue DNA sequence followed by some adjustments from the default values Page 22 ProMOL Users Guide 7 25 11 MacPyMOL MacPyMOL MacPyMOL MacPyMOL
21. rtant to note that in order to have access to plugins and be able to install ProMOL you need to use an X11 version rather than an Aqua version MacPyMOL works both ways In order to tell MacPyMOL to work with X11 and make plugins available you need to rename MacPYMOL app to PyMOLX11Hybrid app first Components The ProMOL interface has 5 tabs Welcome EZ Viz Motif Finder Motif Maker and View Options as well as 6 buttons at the base of the GUI Open Fetch PDB Random PDB Clear and Help that are always available The following pages describe the use of the Buttons and Tabs Page 5 ProMOL Users Guide Buttons on the ProMOL GUI 7 25 11 The buttons on the bottom of the screen appear whenever ProMOL is open Fetch PDB Open PDB Random PDB Clear Help Open PDB opens a dialog box that will let you search any storage devices connected to your computer for PDB files Fetch PDB opens a dialog box that allows you to open a PDB file over the Internet using the PDB Loader Service a plug in that is available on all PyMOL builds If you enter an invalid PDB code you receive an error message You have entered an invalid pdb code followed by the code you entered The sample image was generated by entering zzzz as the PDB code Random PDB loads a PDB file selected at random This is a handy tool if you wish to test for true negatives and false positives when designing and testing motifs see
22. ructures that are under evaluation Press Start to begin search O O Choose A l l C All Motifs Warning Do not click on the results of the Motif Finder while itis still running as this will produce User Motifs incorrect results Also do not load clear or modify any structures or selections while the Motif Finder is C P set running for the same reason set When the search is complete the results will appear in the box on the right side of the Motif Finder tab The results are reported by PDB ID ina scrollable window Cancel Y Figure 9 In the Motif Maker output window the Figure 8 Choosing the motif sets to format for each template is Score_motif group_pdb T template fileid_EC Select Page 12 ProMOL Users Guide 7 25 11 Motif Finder e Score The results are assigned a value ranging from 0 to 4 Each alignment is given a score based on a Levenshtein distance which reflects the number of differences between the query structure 1gtq in Figure 9 and the template motifs that are listed there In simple terms the Levenshtein distance from the word horse to the word house is 1 since you need to change the 34 letter from an r in horse to a u in house In the example shown two structures report a Levenshtein distance of 0 EERE meaning that there are no changes all 2 P_inhc_3_2_1_ B7 of the amino acids in the active site of the temp
23. s may match poorly or not at all In the case of a poor or non existent match the researcher then needs to explore the structure Typical reasons for a poor match are substitutions in the structure perhaps a serine was replace with a lysine by site directed mutagenesis to give a more Stable crystal the absence of the catalytic site homology is based on the entire sequence not just the few residues in the catalytic site or an overly constrained motif maker definition file The next stage in motif testing is a search for false negatives structures that ProMOL incorrectly identifies as containing the motif To that end we usually test the motif against 10 randomly selected PDB files This is done by clicking the Random radio button in the Homolog and Random Testing box then clicking on the test button 10 times The 1j96 motif was tested 10 times on randomly selected files 1dzk 2135 1e4d 2mgc 1pic 1u6j 2eq7 1ztz 1q80 Irkc and none returned an active site For this limited test then no false positives were returned Page 21 ProMOL Users Guide 7 25 11 View Options Users can visit the View Options tab Figure 17 to adjust the way PyMOL generates images of their structures The Preset Views box of the EZ Viz tab enables users to generate interesting views of structures without coding in Python The View Options tab can then be used to adjust the appearance of cartoons spheres sticks and surfaces found ina structure it is als
24. sion 4 2 Release Candidate 2 Welcome EZ Viz Motif Finder Motif Maker Sate Motif Maker PDB 1j96 EC 1 3 1 20 Precision Factor 2 00 1 Residue asp Chain a Number 50 BackBone Off 2 Residue tyr Chain a Number 55 BackBone Off 3 Residue lys Chain a Number 84 BackBone Off 4 Residue his Chain a Number 117 BackBone Off gt 5 Residue Chain Number BackBone Off gt 6 Residue Chain Number BackBone Off gt 7 Residue Chain Number BackBone Off 8 Residue Chain Number BackBone Off gt 9 Residue Chain Number BackBone Off gt 10 Residue Chain Number BackBone Off Order Clear Test Save Export Homolog and Random Testing Homolog C Random Test Open PDB Fetch PDB Random PDB Clear Help As Figure 16 The Motif Maker window with entry locations for four residues in 3a hydroxysteroid dehydrogenase type 3 PDB id 1j96 Once a motif has been entered in Motif Maker it can be tested on the template structure by clicking the test button found in the Motif Maker box A test of this motif yielded an immediate match of only the desired residues If additional residues appear often due to the distance between residues in some catalytic sites there are ways to adjust the motif to select the desired residues First the precision factor can be reduced The precision factor is a multiplier that is applied to the distances between the residues in the catalytic site The next adjustment is mad
25. unch PyMOL and look for ProMOL in the Plugin menu When all files are in place the ProMOL gui can be opened by selecting ProMOL from the plugin menu Macintosh 1 Rename your MacPyMOL application for MacPyMOL ONLY not pymol Under Mac OS X if you have MacPyMOL as opposed to pymol installed using fink or macports you will need use a copy of the MacPyMOL application MacPyMOL app renamed PyMOLX11Hybrid PyMOLX11Hybrid app in order to get access to plugins This is not Page 3 ProMOL Users Guide 7 25 11 necessary for the versions of pymol as opposed to MacPyMOL installed using fink or macports 2 Expand the compressed file 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 3 Plugins that consist of a single python file e g plugin py can be installed simply by using the Plugin gt Manage Plugins gt Install menu However this does not work with ProMOL because you need to install the ProMOL folder as well as the ProMol py file This can be a bit tricky on the Mac so follow these instructions closely if you have MacPyMol renamed as PYMOLX11Hybrid a Find the startup folder in PyMOL i Open Finder gt Applications ii If you have a three button mouse right click on MacPyMOLX11Hybrid and select Show Package Contents This will take you to the directory tree for PyMOL If you don t have a three button mouse Ctrl click should bri
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