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