Greetings Henning, The visible disks & colors in the Mutagenesis Wizard indicate pairwise overlap of atomic van der Waals radii. The intent is to provide a qualitative feedback regarding contacts and bumps.
Short green lines or small green disks are shown when atoms are almost in contact or slightly overlapping. Large red disks indicate signficant van der Waals overlap. Everything else lies between those extremes. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Henning Stehr > Sent: Tuesday, April 29, 2008 7:39 AM > To: PyMOL-users@lists.sourceforge.net > Cc: dinesh.soa...@ed.ac.uk > Subject: [PyMOL] Color codes in mutagenesis wizard? > > Hi, > > I was asked the following question and couldn't find the > answer, can anyone help? > > "When I mutate a buried small amino acid side-chain to a > larger one, it correctly reveals some clashes around that new > side-chain. I suppose the disk shaped clusters mean clashes. > Can someone please confirm this? I was wondering what the > colour of the disk shapes mean (red, green - do they refer to > atom type?), and does the variable size of the disk mean anything?" > > Cheers, > Henning > > ------------------------------------------------------- > Henning Stehr (Dipl. Ing.) > Structural Proteomics Group > Max-Planck-Institute for Molecular Genetics Ihnestrasse 63-73 > 14195 Berlin, Germany > ------------------------------------------------------- > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by the 2008 JavaOne(SM) > Conference Don't miss this year's exciting event. There's > still time to save $100. > Use priority code J8TL2D2. > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java > .sun.com/javaone > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
