Hi Simon - I think I know what the problem is. Is your ligand composed of 'HETATM's? Pymol doesn't include HETATM records in calculating surfaces - this is because most PDB files have waters etc. in them, and Warren wanted the user to be able to load the PDB file and create a surface (for the protein) without a lot of fiddling with selections.
You can, I believe, change this behavior so that Pymol will include HETATM records in surface calculations. I don't remember how, but Warren will probably chime in. The workaround is to substitute 'ATOM ' for 'HETATM' for the atoms in question... - Matt pymol-users-boun...@lists.sourceforge.net wrote on 11/02/2006 09:58:30 AM: > No. When I read in the pdb, containing the ligand and the protein > and simply calculate the surface, I get a surface for the protein, > but not the ligand. > > Simon > > > > > On Nov 2, 2006, at 3:53 PM, Nicholas Noinaj wrote: > > > can you get a surface for the protein-ligand complex? > > > > > > > > cheers, > > nick > > > > -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
