[chimerax-users] Questions about ChimeraX and problems re-downloading Chimera

[Elaine Meng]

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 at 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