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Re: [PyMOL] [PyMol] How to visualize surface within a given radius
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From: Sampson, J. <Jar...@ny...> - 2013-03-04 20:40:48
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Hi Yarrow - If you add "br. " to the show surface command, you will get more continuous surfaces, as the selection will be made by residue instead of by atom. show surface, br. protein within 0.5 of pocket_selection If you don't want to show the surface from a particular residue (e.g. if it's masking something else you want to show), you can hide surface for a selection. hide surface, resi 225+347 Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 4, 2013, at 2:37 PM, Yarrow Madrona <ama...@UC...<mailto:ama...@UC...>> wrote: Thank you for your help Thomas, Using your settings I get a lot of "partial surfaces" Showing the surface around the Pocket selection like this: show surface, protein within 0.5 of pocket_selection worked well but I still see a piece of surface that I really don't want to show up. I guess I can take it out in photoshop but that just seems wrong. I have attached it. -Yarrow Hi Yarrow, should be as simple as: PyMOL> hide surface PyMOL> show surface, (organic around 8.0) PyMOL> set transparency, 0.3 PyMOL> set two_sided_lighting See also: http://pymolwiki.org/index.php/Selection_Algebra Hope that helps. Cheers, Thomas Yarrow Madrona wrote, On 03/03/13 18:34: Hello, Does anyone know how to visualize a surface within a given radius from a ligand binding site? In chimera you can limit the display surface within 0-X angstrom of a ligand. This allows you to see the surface surrounding the ligand without the rest of the protein. I guess you could create a new selection of residues around a ligand and show this surface but I wondered if there are any other ways of doing this. -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 <screenshot.png>------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
