Thank you both for your kind help. I will follow this up today and let you know how it goes.
-Yarrow > Greetings, > > Please also investigate the following settings: > > # needs a real atom selection > surface_carve_selection > > # distance from the above selection to cull surfaces > surface_carve_cutoff > > I looked at your data and there is a small problem. You have a few points > where one atom is mapped to multiple surface points. Thus, when you show > it > as surface two pocket fragments show up. When you hide it they both hide. > > Also of interest is PyMOL's ability to render pockets and cavities on its > own (Settings > Surface > Cavities & Pockets). > > Cheers, > > -- Jason > > > On Mon, Mar 4, 2013 at 2:15 PM, Sampson, Jared > <jared.samp...@nyumc.org>wrote: > >> 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 <amadr...@uci.edu> 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 (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> >> -- >> 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 (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> >> >> >> ------------------------------------------------------------------------------ >> 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 (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Products > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 ------------------------------------------------------------------------------ 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
