[Chimera-users] Defining Attribute Color for Surface Independent of Atoms

[Elaine Meng]

On Tuesday, January 25, 2005, at 10:14 AM, David Piper wrote:
>   I have set up a file to define a series of colors based on  
> functional measurements for some residues in a PDB file.
>   I would like to color the ball and stick atoms according to element  
> type and a semi-transparent surface according to the colors defined by  
> my text file.
>   It seems like these two things are tied together; that the surface  
> can either be colored by the model, the atoms, or a specific color.
>   Can I color it according to a Defined Attribute but leave the atoms  
> as CPK coloring?

Dear David,
Yes, the surface can be colored separately from the atoms.  If you
already used Define Attribute to create your attribute, then just
use the Colors section of Render by Attribute (Tools... Graphics...
Render by Attribute).  Uncheck the box to "Color atoms" and make
sure the "Color surfaces" button is checked. The coloring will then
be applied to just the surface.

The manual page for Render by Attribute:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ 
render.html

You could do basically the same thing with the command "rangecolor"  
where
putting ",s" right after the attribute name indicates that coloring  
should
apply to the molecular surface.

The manual page for rangecolor:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html

Another way is to use Define Attribute to assign values directly to the
atom attribute "surfaceColor"  ("color" is the atom color,  
"surfaceColor" is
the color of that atom's surface, and they don't have to be the same
as each other).  The last example file linked to the Define Attribute  
shows
a similar approach.

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ 
rescol.txt

I hope this helps,
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