Hi Steve, Our system was down for a few days after a hardware failure, but it’s up again now.
Neither Chimera nor ChimeraX has a command to color by all of the amino acid types in a single command. Of course, you could easily color some specified type however you wish, e.g. in ChimeraX:
color :cys spring green
...or to color only the atoms (not ribbons, surface patches, etc.):
show :cys color :cys orange red target a
http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html
Also, we do provide (for ChimeraX) command files that will color amino acids by some standard schemes and one I made up myself. You could just download any of those and open it (e.g. with the “open” command) to apply the coloring, and/or edit it first to customize the scheme:
http://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#residue
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 19, 2018, at 6:28 AM, Steven Douglas Aird steven.aird@oist.jp wrote:
Dear Elaine, Is there a way in ChimeraX to specify colors for individual species of amino acids? I would like to color cysteine residues to illustrate disulfide bonds. There appears to be no ‘byresidue' or ‘byaminoacid’ command. Since I had formerly done this in Chimera, I sought to re-download that from: https://www.cgl.ucsf.edu/chimera/download.html This page has been unresponsive for hours and the download cannot be completed.
Thanks for your help, as always. Sincerely yours, Steve Aird