[Chimera-users] Color surface by underlying atom

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 6 10:17:44 PDT 2016


Hi Tom,
It is a little complicated because molecular surfaces can have per-atom coloring (i.e. the “patch” of surface next to a particular atom can be colored differently from the other surface patches), but those colors are not necessarily the same as the colors of the atoms themselves.  The specific answer depends on what surface coloring you are trying to get back to.  Chimera does not have a command that makes the surface per-atom colors the same as the colors of the corresponding atoms.  There are some related commands; for example

~color,s

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>
… will remove the coloring that you did, but then it will show the single model color.  Maybe that is what you meant.  Another thing you could try, but I doubt it will give what you want, is:

surfcolor byatom

… but that does not necessarily mean that the surface will have the same coloring as the atoms, only that it has per-atom coloring.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surfcolor.html>

Probably you would need to do it the hard way: repeat the coloring commands or actions that gave the atoms those colors.  By default, those commands would color the molecular surface and the atoms at the same time.

Coloring hierarchy:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/hierarchy.html>

Sorry I don’t have a more direct answer,
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 Jul 6, 2016, at 9:31 AM, Tom Zhang <yzhan197 at jhu.edu> wrote:

> Hello,
> 
> I have a question about surface coloring.
> I've noticed that when I create surfaces in a session for the first time, the surface are colored based on the colors of the underlying atoms. However, after setting the surface colors manually, I couldn’t find a way to change the colors back. I have tried settings in surface attributes, but none of them work.
> 
> So my question is, how do I change the surface color back so that it is based on the underlying atoms?
> 
> Many thanks,
> Tom




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