[PyMOL] Interaction surfaces
I have a problem representing the contact surface between, e.g., a protein and its ligand. The surface is displayed, but it is full of holes, apparently at the points of contact. The script: load protein.pdb, protein load ligand.pdb, ligand hide everything show surface, (protein and (ligand around 4)) gives something like one wants, but full of holes. With that object displayed, if one says show surface, protein one gets the full surface, without the holes. Any ideas on how to get the *partial* surface *without* the holes? Joe Becker Merck Research Labs P.S. load protein.pdb, protein load ligand.pdb, ligand hide everything create junk, (protein and (ligand around 4)) show surface, junk gives a similar (holey) result -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (Whitehouse Station, New Jersey, USA) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it. --
RE: [PyMOL] Interaction surfaces
Joe, Currently with PyMOL, you are selecting are atoms, not points on the surface. Thus, you may need to increase the distance by 1-2 A or so to get what you want. It's also possible that something else is going on. I would not expect to see whole at the points of contact, but between them, where the contacts aren't so close. If the above advice doesn't help, then perhaps you could send me an example PNG file which illustrates the problem as an attachment? Cheers, Warren (PS. Selection of individual surface points will likely come in a future version...) -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Becker, Joseph W Sent: Friday, July 11, 2003 10:45 AM To: PyMOL (E-mail) Subject: [PyMOL] Interaction surfaces I have a problem representing the contact surface between, e.g., a protein and its ligand. The surface is displayed, but it is full of holes, apparently at the points of contact. The script: load protein.pdb, protein load ligand.pdb, ligand hide everything show surface, (protein and (ligand around 4)) gives something like one wants, but full of holes. With that object displayed, if one says show surface, protein one gets the full surface, without the holes. Any ideas on how to get the *partial* surface *without* the holes? Joe Becker Merck Research Labs P.S. load protein.pdb, protein load ligand.pdb, ligand hide everything create junk, (protein and (ligand around 4)) show surface, junk gives a similar (holey) result -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (Whitehouse Station, New Jersey, USA) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it. -- --- This SF.Net email sponsored by: Parasoft Error proof Web apps, automate testing more. Download eval WebKing and get a free book. www.parasoft.com/bulletproofapps1 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] how to get minimum distances in script?
Hello all, I am trying to write a script that will go through each residue in a dimer interface and determine for each one how close it is to the partner monomer. I can interactively plot all the distances within a certain cutoff using the handy: distance chosen, residue_selected_on_first_chain, partner_monomer_selection, cutoff For atom selections Warren earlier explained how to parse into its components (using list=[]; iterate (selection),list.append((resi,resn))). However, the selection created by the distance command (i.e. chosen) does not behave the same way it seems and I haven't been able to iterate over it to get at the info. I see from help distance that in the API cmd.distance returns the average, so it suggested that perhaps minimum and maximum or even each individual value might also be accessible, giving me hope that the more elegant solution was close at hand and limited more by my ignorance than the chosen approach. Otherwise I suppose there's the more brute-force avenue of going through each residue, selecting atoms from the partner monomer within a certain distance if any, and then explicitly measuring the distance to each atom one by one, but I thought I'd check with the community before launching such an ugly attack on the problem, having walked that road before! Also, not to push my luck, but if you'd like to write your suggestions in both English and Python, my less-than-rudimentary knowledge of Python will thank you(!) Cheers and thanks, Seth -- ~ Seth F. Harris, PhD Agard Laboratory University of California, San Francisco Mission Bay Genentech Hall 600 16th St. Suite S416 San Francisco, CA 94143-2240 415.502.2930
