[PyMOL] Showing only part of a surface around a ligand
Hi all, this question may be resolvable by sufficient RTFMing, but maybe there is someone out there to help me... I am trying to generate a figure in which I want to show only a part of the protein surface around a ligand - pretty much like preset -- ligand sites -- solid surface I have already tried some amateur solutions like splitting the ligand into parts, placing waters to generate pseudo-ligand atoms and the like. Somewhat unsatisfying. I have also realized that I can click on every atom of the protein and do a show surface, but this will drive me insane sooner than later. I guess it must be doable through some magic selection commands - if I could only see how the preset command works, I could probably work it out from there. Can somebody please point me in the right direction? Thanks in advance, Wulf
Re: [PyMOL] Showing only part of a surface around a ligand
Wulf, suppose you have this scenario: Protein in chain A Ligand in chain I Then create b-site, byres chain A within 5 of chain I show sticks, chain I show surface, b-site should get you close. HTH Carsten BTW If you replace the create command with select your surface will be scribed i.e. with frizzled ends. If this is what you want then you should use select. -Original Message- From: Wulf Blankenfeldt [mailto:wulf.blankenfe...@mpi-dortmund.mpg.de] Sent: Wednesday, March 25, 2009 1:31 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Showing only part of a surface around a ligand Hi all, this question may be resolvable by sufficient RTFMing, but maybe there is someone out there to help me... I am trying to generate a figure in which I want to show only a part of the protein surface around a ligand - pretty much like preset -- ligand sites -- solid surface I have already tried some amateur solutions like splitting the ligand into parts, placing waters to generate pseudo-ligand atoms and the like. Somewhat unsatisfying. I have also realized that I can click on every atom of the protein and do a show surface, but this will drive me insane sooner than later. I guess it must be doable through some magic selection commands - if I could only see how the preset command works, I could probably work it out from there. Can somebody please point me in the right direction? Thanks in advance, Wulf -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Showing only part of a surface around a ligand
Wulf, The source code for presets can be found in modules/pymol/preset.py, but there is object, method, and housekeeping stuff in there that distracts from its understandability. show surface, polymer within 5 of organic May be all that you really need. # example use load $TUT/1hpv.pdb hide show surface, polymer within 5 of organic set two_sided_lighting show lines, byres polymer within 5 of organic show sticks, organic color auto, organic and elem c set transparency, 0.3 Cheers, Warren -Original Message- From: Wulf Blankenfeldt [mailto:wulf.blankenfe...@mpi-dortmund.mpg.de] Sent: Wednesday, March 25, 2009 10:34 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Showing only part of a surface around a ligand Hi all, this question may be resolvable by sufficient RTFMing, but maybe there is someone out there to help me... I am trying to generate a figure in which I want to show only a part of the protein surface around a ligand - pretty much like preset -- ligand sites -- solid surface I have already tried some amateur solutions like splitting the ligand into parts, placing waters to generate pseudo-ligand atoms and the like. Somewhat unsatisfying. I have also realized that I can click on every atom of the protein and do a show surface, but this will drive me insane sooner than later. I guess it must be doable through some magic selection commands - if I could only see how the preset command works, I could probably work it out from there. Can somebody please point me in the right direction? Thanks in advance, Wulf -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
