From: Andrew D. F. <fa...@po...> - 2007-08-31 21:55:01
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Is there an easy way to refer to/select a portion of a molecular surface that is within a given distance of another molecule's surface? I'm trying to generate some graphics for a presentation on a signaling pathway, and I want to show just the part of each peptide's solvent accessible surface that is making contact with the binding site. Ideally, I would like to be able to color this, at least in a contrasting color to the structures of the components, but preferably tied to electrostatic potential or hydrophobicity. Has anyone ever done this, and if so, can you spare any advice? Thanks, Andy |
From: Tsjerk W. <ts...@gm...> - 2007-09-01 07:28:38
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Hi Andy, Do you mean something like: show surface, byres Obj1 within 3 of Obj2 show surface, byres Obj2 within 3 of Obj1 Be sure to have the peptide and the protein as separate objects, otherwise this won't work. You can of course also drop the 'byres' statement if you want... Hope it helps, Tsjerk On 8/31/07, Andrew D. Fant <fa...@po...> wrote: > Is there an easy way to refer to/select a portion of a molecular > surface that is within a given distance of another molecule's surface? > I'm trying to generate some graphics for a presentation on a signaling > pathway, and I want to show just the part of each peptide's solvent > accessible surface that is making contact with the binding site. > Ideally, I would like to be able to color this, at least in a > contrasting color to the structures of the components, but preferably > tied to electrostatic potential or hydrophobicity. Has anyone ever > done this, and if so, can you spare any advice? > > Thanks, > Andy > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 |
From: Andrew D. F. <fa...@po...> - 2007-09-02 20:46:47
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Thanks Warren and Tsjerk for your hints. This will keep me busy for a while playing with options. Andy Andrew D. Fant wrote: > Is there an easy way to refer to/select a portion of a molecular > surface that is within a given distance of another molecule's surface? > I'm trying to generate some graphics for a presentation on a signaling > pathway, and I want to show just the part of each peptide's solvent > accessible surface that is making contact with the binding site. > Ideally, I would like to be able to color this, at least in a > contrasting color to the structures of the components, but preferably > tied to electrostatic potential or hydrophobicity. Has anyone ever > done this, and if so, can you spare any advice? |