[Chimera-users] multiple mutations

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 29 15:58:08 PST 2016


Hello Andrew,
You could just specify 100 residue numbers in a coloring command, except that would make them all the same color.  For a smaller example, the following command would color red the atoms-only (not ribbons) of residues 10 and 34 in chain A and residue 255 in chain B:

color red,a :10.a,34.a,255.b

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

Or you could give 100 coloring commands each with a different color.  There is no Chimera command for random coloring.  Chimera can execute Chimera-command files or python files, but you’d still have to specify all the residue numbers and colors somehow.

A weirder idea is to assign each mutated residue a unique value of some “attribute”, for example ranging from 0-1 where no two residues have the same value, and then in a single “rangecolor” command you can map that numerical range to a range of colors.   As long as the values were unique, the colors would be too. However, you’d still need 100 “setattr” commands or  a single attribute-definition file (see links below), and those would still need the 100 residue numbers in them.  The possible advantage would be that only a single “rangecolor” command is needed to then color all the residues, and you can try it with different colormaps without having to reassign the values.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>

A common use of rangecolor-by-attribute is coloring to show B-factor values.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.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 Feb 28, 2016, at 8:22 AM, Andrew N <derm101 at live.com> wrote:
> 
> Hello:
> How can mark (change color) for ~ 100 mutations at once?
> Is it possible to write a "code" for that? 
> I would like to have random (different) colors for every mutation. It the case, if mutation lay down very close and same color would make it difficult to tell them apart.
> 
> Another question: How to add a label like "V75" (Amino acid and position, not "V75.A") with all with black color (not the same color that marks mutation on 3D structure)?
> 
> Thank you.
> Sincerely,
> Andrew 
> 



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