[Chimera-users] Defining Attribute Color for Surface Independent of Atoms
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:
> 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:
> 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
> a similar approach.
> I hope this helps,
> 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
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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