[chimerax-users] pdb and map colors

[Elaine Meng]

Hi Andrey,
Yes, you can show the sequence with “sequence chain”  followed by chain-spec, e.g. with a command like:

seq chain /A
seq chain #5/H

<http://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html>

Drawing a box in the sequence will select the corresponding parts of the structure like it does in Chimera.  You probably already know you can use the “color” command to color your selection (or alternatively, you can specify chains/residues/atoms directly in the command), e.g.

color sel pale green

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>

Then you can color a map surface to match nearby atoms with “color zone”, e.g.

color zone #2 near #5 dist 5

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>

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 25, 2018, at 3:50 PM, Andrey Feklistov <afeklistov at mail.rockefeller.edu> wrote:
> 
> My question is about ChimeraX 0.6: is it possible to highlight different parts of a pdb (based on the protein sequence) with different colors and then color a corresponding map accordingly. I can't find an option 'Sequence' like in the old Chimera, is it possible to do this from a command line?
> Thanks!