Greg, You can also use the alter command to change the vdw to the value you want. This is often done with SAXS bead models so that they can then be surfaced.
alter (n. ca), vdw= 3 If this is set after the show spheres command the rebuild the view rebuild Hope this helps. Best regards, Mark Sent from my iPhone On Jul 26, 2013, at 4:12 PM, "Sampson, Jared" <jared.samp...@nyumc.org<mailto:jared.samp...@nyumc.org>> wrote: [Re-posting to the list because, as usual, I forgot to Reply All...] Hi Greg - If I understand correctly (and just on a quick visual inspection in PyMOL it looks like I'm at least close), the sphere_scale setting will scale the size of the sphere relative to the van der Waals radius of the atom. So at sphere_scale == 1, Carbon will be ~1.70Å, Oxygen will be ~1.52Å, Nitrogen ~1.55Å, and so forth. To have a CA atom of 3Å radius, you would use sphere_scale of ( 3.0 / 1.7 ) = 1.76. Hope that helps, 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 Jul 26, 2013, at 3:23 PM, Gregory Ryslik <rsa...@comcast.net<mailto:rsa...@comcast.net>> wrote: Hi, I'm a fairly new user to PyMol and am having some trouble with the sphere_scale command. I understand that if I want to draw a sphere around the x'th ca atom, I can use: show spheres, ////X/ca However, what if I want that sphere to have a radius of 3 angstroms, or 6 angstroms, etc. I understand I can use set sphere_scale, 1, ///X/ca but what is the default scale of 1? Is it 1A, is it something else? Thank you for your help! Kind regards, Greg ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto: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 ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto: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 ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ 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
