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

Melissa Jurica mjurica at ucsc.edu
Sat Sep 3 11:23:15 PDT 2016

Thanks Elaine-

My structures have more than 20 individual components (recent spliceosome cryo-EM models- example PDB 5GMK).  They came as 1 model, which I split to have more control over for analysis.  I can go through each component by hand and copy/paste the color for each model into a text file and then turn then this into a command file to color another structure with the same components in another conformation.  (Thanks for turning me on to the “modelcolor” command.  That will be helpful!) However, I was hoping there was a way to use something like grep to extract this information from the .py session file.


Melissa S. Jurica, Ph.D.
Professor, Molecular, Cell & Developmental Biology
Center for Molecular Biology of RNA
University of California, Santa Cruz
1156 High Street
Santa Cruz, CA 95064

Office: 450 Sinsheimer Labs	Lab: 434 Sinsheimer Labs 
Office phone (831) 459-4427	Lab phone (831) 459-2463	Fax (831) 459-3139

On Sep 2, 2016, at 5:11 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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