[Chimera-users] color by zone in chimeraX

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 20 11:47:16 PDT 2019

Hi Pranav,
I’m Cc'ing the chimerax-users at cgl.ucsf.edu list (recommended for ChimeraX questions).

I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding.

If you use “target ac”  instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect.  


I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab at gmail.com> wrote:
> Hi Elaine and Co.,
> I am trying to color a virus map with the relevant pdb file, the
> series of commands I am running are as follows,
> open virus.mrc
> open virus.pdb
> color /A plum target c
> color /B lightgreen target c
> color /C dodger blue target c
> color zone #1 near #2  dist 3
> However, the resultant surface is rendered in splotches of red and
> blue, which leads me to think the it is coloring the surface using
> atom type. Could you tell me how I can get Chimera X to color the
> surface using the colors of the chains only? FYI, color by zone works
> flawlessly in chimera.
> Cheers,
> Pranav

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