Dear Marcelo, * castilho <casti...@if.sc.usp.br> [2004-08-23 17:02] wrote: > My name is Marcelo and I am a basic-level pymol user. I work with docking > programs and I am trying to make pymol our default program for analysing > docking results...this brings me to some questions: > > Is it possible to colour protein surface according to Hydrogen > donor/acceptor properties in pymol ?
I guess that depends on whether you can define what constitutes a donor or acceptor easily enough. I think with sufficient logical operations you could. For example: select donor, name N or (resn ASN and elem N) or (resn GLN and elem N) etc. Then you could colour the "donor" selection as you like. > Does Pymol computes a ligand-protein interface (for example just the contact > area between the ligand and the protein)? is it possible to see just this > surface area according to the previous question schema ? If you have the ligand and protein in separate objects, let's call them ligand and protein, you can do this: show surf, ligand within 3. of protein show surf, protein within 3. of ligand where it will show the surface only for atoms within 3 Angstroms of the other molecule. You could also include the "byres" keyword which might remove some holes in the surface if desired: show surf, byres ligand within 3. of protein If the structure file you read in contains both, then you can create separate objects from the single initial object: create protein, initial and chain A create ligand, initial and chain B where I'm assuming that the protein has the "A" chain identifier and the ligand has the "B" chain identifier and the initial object was called "initial". > Does pymol read grid (Goodford's grids) ? in case not, how can I convert > GRID maps into something pymol can read ? It appears that you can convert Goodfords grid format to other map formats (e.g. Brix and CCP4) using the Bsoft program package: http://www.niams.nih.gov/rcn/labbranch/lsbr/software/bsoft/bsoft.html The software contains the code for reading and writing GRID files, so perhaps that could be incorporated into PyMOL. (I couldn't find any license file, though I suppose the author could be contacted directly.) Hope this helps. Cheers, Rob -- Robert L. Campbell, Ph.D. <r...@post.queensu.ca> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
