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

Sabuj Pattanayek sabuj.pattanayek at vanderbilt.edu
Tue Jan 25 15:22:01 PST 2005

This might be simpler, but in situations like these I just open the pdb 
file again, use one model say #0 for defining the colors on the 
atoms/bonds, and model #1 for defining colors on the surface. You can 
then turn the atoms/bonds display off for your surface (model #1).

Elaine Meng wrote:
> 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
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