[Chimera-users] Specifying residue color of residues with a text file

[Elaine Meng]

  Hi David,
You can specify residues and corresponding R,G,B values using
Define Attribute, which is included in our newer releases
(snapshot 1.2029 and production release 1.2038, of which I
recommend the latter).  Basically, this tool reads a file 
that specifies the residues and the associated values.

The manual page for Define Attribute can be viewed at:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html

including three examples near the end:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#examples

There are two general approaches you may want to consider:

(1) the direct approach that you described.  Just reassign
R,G,B values to the existing attribute of atom color and/or
residue ribbonColor.  This is most like the third example,
except that you would use residue specifications by number
(e.g., :12.A) instead of name, and the color specifications
would be in the form of R G B (e.g., 1.0 0.2 1.0) instead of
color names.

(2) a less direct approach but one that provides more flexibility
in how you show the data.  Create your own new attribute (as in
the first example).  Then, you can use Render by Attribute
(http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html)
to show these values with colors, atom radii, and/or "worm" radii.
The data will show as a histogram, and the mapping to colors and 
radii can be controlled with markers you place on the histogram.

This may be a lot to digest, so please feel free to contact
us with any further questions/issues.
  Thanks,
    Elaine
-------------------
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html