Hello Andrew, You could just specify 100 residue numbers in a coloring command, except that would make them all the same color. For a smaller example, the following command would color red the atoms-only (not ribbons) of residues 10 and 34 in chain A and residue 255 in chain B: color red,a :10.a,34.a,255.b <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> Or you could give 100 coloring commands each with a different color. There is no Chimera command for random coloring. Chimera can execute Chimera-command files or python files, but you’d still have to specify all the residue numbers and colors somehow. A weirder idea is to assign each mutated residue a unique value of some “attribute”, for example ranging from 0-1 where no two residues have the same value, and then in a single “rangecolor” command you can map that numerical range to a range of colors. As long as the values were unique, the colors would be too. However, you’d still need 100 “setattr” commands or a single attribute-definition file (see links below), and those would still need the 100 residue numbers in them. The possible advantage would be that only a single “rangecolor” command is needed to then color all the residues, and you can try it with different colormaps without having to reassign the values. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile> A common use of rangecolor-by-attribute is coloring to show B-factor values. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 28, 2016, at 8:22 AM, Andrew N <derm101@live.com> wrote:
Hello: How can mark (change color) for ~ 100 mutations at once? Is it possible to write a "code" for that? I would like to have random (different) colors for every mutation. It the case, if mutation lay down very close and same color would make it difficult to tell them apart.
Another question: How to add a label like "V75" (Amino acid and position, not "V75.A") with all with black color (not the same color that marks mutation on 3D structure)?
Thank you. Sincerely, Andrew