[Chimera-users] coloring the clipped surface

[Elaine Meng]

On Feb 22, 2009, at 4:48 PM, Harinathachari Bahudhanapati wrote:
> Dear Elaine,
> Chimera is getting more exciting to work with than
> ever. I think you guys are the best in the field.
> About per-model clipping...
>
> When I tried, I was not able to find how to color the clipped plane
> based on atom B-factors? I was able to give a color (single color)  
> only
> but not based on atom B-factors or other attributes like SAS, SES,
> electropotential.
> I am not sure if modeled PDB files still have B-factor details. I saw
> an image on the chimera website on the feature highlights (B-factor
> coloring) and I wondered if I can get few more details on this  
> feature.
> I am trying to make a few pictures for my paper.
> Thank you elaine,
> sincerely,
> Hari
>

Dear Hari,
Thanks for your kind words!

Yes, there is a trick to coloring planar surface caps by B-factor or  
some other attribute, as in that figure:
<http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png>

First, color the atoms by the attribute (Tools... Depiction... Render  
by Attribute), which would also color the actual molecular surface  
but not the planar cap where it is clipped.  Then, select the atoms  
and use Color Zone (also under Tools... Depiction) to color the  
planar cap to match the nearby atoms.

Render by Attribute:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ 
render.html#render>
Color Zone:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/ 
colorzone.html>

I've been wanting to write a tutorial on how to make that figure, but  
haven't had the time!  I also increased the "mesh subdivision factor"  
in the Surface Capping dialog to 3.

Coloring by electrostatic potential is different than coloring by an  
atom attribute.  To color the planar cap by electrostatic potential,  
you would use Electrostatic Surface Coloring, but it requires a  
potential map previously created with some other program such as DelPhi.

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