[Chimera-users] extracting chaing colors from session file?

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 2 17:11:32 PDT 2016


Hi Melissa,
At first I was going to suggest “mcopy” but from your description, it sounds like you have each chain as a separate model.  “mcopy” is only for copying settings within one model to other models.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.html>

You can get the current atom-color RGB definitions or hex codes by Ctrl-click to select an atom (or ribbon segment to select the whole residue, if all of its atoms are the same color), showing the Selection Inspector, Inspect: atom, and then clicking the square color well to get the Color Editor.  Then in the Color Editor you can see the hex code starting with # in the “Color name” field.

The square in the Model Panel shows the model-level color.  Chimera has a coloring hierarchy, where if the atoms are individually assigned colors (such as with your color command), in the 3D display those colors mask the model-level color, which may be different.  You can use the modelcolor command, for example “modelcolor #6168c8fb41bc #0.17” or click the color square in the Model Panel to make the Color Editor dialog appear, and then enter the hex code in the “Color name” field of the Color Editor: 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortool.html>
There is only one model-level color per model, as the name suggests, even though the atoms and per-residue ribbon segments might be all different colors.

More about color hierarchy:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/hierarchy.html>

I hope this helps,
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 Sep 2, 2016, at 1:23 PM, Melissa Jurica <mjurica at ucsc.edu> wrote:

> I am analyzing a structure containing many individual chains that I have colored.  I would like to transfer these colors to another structure of the same complex in a different conformation.  Is there a way to extract the colors into a text file so that I can write a command file with the same color designations?
> 
> For example:
> 
> color #6168c8fb41bc #0.17
> 
> Also-
> How do I get that color to apply to the little square that shows up on the model panel?
> 
> Melissa




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