This would be great. I'm more than a bit rusty with programming, so I'm not sure I'd be able to figure out how to build a pymol plugin. But I'd be happy to provide the cgo generating script or answer questions about reduce or probe. -bob
On Wed, Oct 22, 2014 at 2:11 PM, Tim Schulte <tim.schu...@ki.se> wrote: > 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> > 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) >> 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) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (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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