[Chimera-users] coloring protein structure according to Order parameters

[Elaine Meng]

Dear Ramakrishna,
It sounds like you want to use "Render by Attribute" to show values  
with color.  Some attributes are created automatically by Chimera  
(for example, atom B-factor or residue hydrophobicity), but you can  
also create your own attributes and use this same tool for coloring.   
It shows the values in a histogram, and you can adjust the coloring  
by moving vertical bars on the histogram and changing their colors.   
You can also show values with ball radii and "worm" fatness.

"Render by Attribute" man page:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ 
render.html

"rangecolor" command (also does coloring by attribute value):
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html

"Define Attribute" man page (how to create your own attributes):
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ 
defineattrib.html

Basically it reads in a simple text file with your assignments; the  
format is described and example files are included.

The "Attributes" tutorial includes examples of using Render by  
Attribute and other related tools:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
attributes.html

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Jan 3, 2008, at 1:43 AM, rama krishna wrote:

> Dear Friends,
>
> I need to Paint a protein structure according to generalized  
> parameter values.
>
> Is there any way to do that in UCSF-Chimera.
>
> Kindly suggest me.
>
> Regards
> Ramakrishna,
> Dr Ashish Arora Lab,
> Molecular and Structural Biology lab,
> Central Drug Reseach Institute,
> India
>
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