Hi Robert, I did something like this in the past. Check out the ramp_new command page on the PyMOLWiki for an example (http://pymolwiki.org/index.php/Ramp_new#Elaborate_examples) for arbitrary functions.
Here's a very quick way to color a surface by distance from a given point--here I chose the origin (0,0,0): # fetch a friendly protein fetch 1hug, async=0 # show it as a surface as surface # create a pseudoatom at the origin; we will # measure the distance from this point pseudoatom pOrig, pos=(0,0,0), label=origin # create a new color ramp, measuring the distance # from pOrig to 1hug, colored as rainbow ramp_new proximityRamp, pOrig, selection=1hug, range=[5,65], color=rainbow # set the surface color to the ramp coloring set surface_color, proximityRamp, 1hug # some older PyMOLs need this recoloring/rebuilding recolor; rebuild Cheers, -- Jason On Thu, Jul 28, 2011 at 10:29 AM, Muench, Robert <robert.mue...@pei.de> wrote: > Dear community, > > > > I was searching the internet for several days now to find out how to > perform a distance dependent coloring in pymol. > > The idea is to color the surface of a viral (spherical) structure. I would > like to define the xyz-coordinates of the center of the viral structure an > color all residues with a gradient depending on the distance from these xyz > coordinates. > > Can anyone please help me out? > > > > All the best > > > > Robert > > > > > > Robert Münch > > --------------------------------------------------------- > > Dipl. Biologist / PhD-Student > > Paul-Ehrlich-Institut > > Federal Institute for Vaccines and Biomedicines > > Division of Medical Biotechnology > > Section 6/5 - Viral Gene Transfer Medicinal Products > > 63225 Langen, Germany > > > > Phone: +49-6103-77-4222 > > Fax: +49-6103-77-1255 > > --------------------------------------------------------- > > > > ------------------------------------------------------------------------------ > Got Input? Slashdot Needs You. > Take our quick survey online. Come on, we don't ask for help often. > Plus, you'll get a chance to win $100 to spend on ThinkGeek. > http://p.sf.net/sfu/slashdot-survey > _______________________________________________ > 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 PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey _______________________________________________ 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
