Tim: Good suggestion, I would second this effort. Thanks for raising the issue
Cheers, Carsten From: Tim Schulte [mailto:tim.schu...@ki.se] Sent: Wednesday, October 22, 2014 2:11 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to draw clashes in pymol -> integration/plug-in of Molprobity in PyMol??? Hej everybody, my question is related to this post. I am just analyzing a structure and really like the way Molprobity puts out information about hydrogen bonds and vdW contacts and so on. It is also possible to take advantage of this analysis in phenix during/after refinement, because Coot provides a graphical interface for visualization of the Molprobity output - however, Coot is not my favorite program for making nice figures. So I just wonder whether it might be of general interest to the pymol community if someone would write a plug-in to integrate the Molprobity output in PyMol? I can definitely not do it, but maybe this could be an interesting feature request to the PyMol developers? All the best, Tim Am 30/08/14 01:53, schrieb Robert Immormino: Hi Bondurant, I really like the merging of the graphic beauty of pymol with the detailed depictions of reduce and probe. I have a method that is a bit clunky for doing what you ask, but I don't know if it ever made it to the mainstream in MolProbity. The caveat of wanting to work with a ligand makes it a bit harder to explain so my apologies in advance if things aren't 100% clear but here goes.... 1. Make sure you have a reduce definition file for your ligand. If the ligand had been deposited in the PDB before ~2012 then the reduce_wwPDB_het_dict file found (http://kinemage.biochem.duke.edu/software/reduce.php) should have it, otherwise here's an example: RESIDUE ACP 11 CONECT P 4 O1 O2 O3 O4 CONECT O1 1 P CONECT O2 1 P CONECT O3 1 P CONECT O4 2 P C1 CONECT C1 3 O4 O5 C2 CONECT O5 1 C1 CONECT C2 4 C1 HC1 HC2 HC3 CONECT HCH1 1 C2 CONECT HCH2 1 C2 CONECT HCH3 1 C2 END HET ACP 8 HETNAM ACP ACETYL PHOSPHATE FORMUL ACP C2 H3 O5 P1 2- 2. download the reduce and probe executables also from http://kinemage.biochem.duke.edu/ 3. run reduce make sure to use the -DB flag to input your ligand dictionary 4. run probe with a command something like: probe -both "chaina 88 (ATOM_OG1 | ATOM_HG1)" "chainx 1" CheY_A88T_AcP_H.pdb Where chain A in this case is the protein and the hydroxyl of Thr 88 is the only relevant interacting group with chain X the ligand. 5. convert the probe output to a python script to render the cgo objects in pymol using the attached perl script. ./probe_to_cgo [input probe dots] [output pymol cgo] 6. use the run command in pymol to execute the python script and draw the cgo output. If this all works the first go then amazing! If not I can try to help get things working, but it's been a few years since I last used these tools. Best of Luck! -bob On Fri, Aug 29, 2014 at 10:30 AM, Bondurant <bondurant...@gmail.com<mailto:bondurant...@gmail.com>> wrote: Hello community, I would like to draw a figure similar to this one http://www.cell.com/cms/attachment/615980/4968633/gr1.jpg showing the clashes between a potential ligand and the protein. The only way i know how to do this in pymol is using the show_bumps plugin, but i don't really like the "red disks" format. Could anyone tell me how i could easily draw something similar to those red spikes from the example to represent the clashes in pymol or any other program? I'm able to do it using molprobity and kinemage, but there's no much possibilities for editing and to get it in printing quality. Thanks ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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