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 > > >
