[Chimera-users] identifying residues in a surface

[Elaine Meng]

On Dec 21, 2009, at 5:14 PM, gytjyb wrote:

> hello:meng!
> thank you for your help!
> i want to make a surface about protein.
> i want to do lipophilicity and electrostatics surface,we had better   
> label some amino acid on the surface,how can i do?
> or i just use differrent color for different amino acid  category.
> i think the color must be very different from each.
> so i can recognize each other,and find out some important different  
> between homology protein.
> thank you very much!
>

Hello,
It is better to send Chimera questions to chimera-users at cgl.ucsf.edu  
(instead of to me directly) and include a short description in the  
"Subject" line.

You can show lipophilicity on the surface with menu item "Presets...  
Interactive 3 (hydrophobicity surface)" where orange is most  
lipophilic and blue is most hydrophilic.

You can show Coulombic electrostatic potential on the surface with  
"Tools... Surface/Binding Analysis... Coulombic Surface Coloring"

The regular labels are not that good when you are showing a surface.   
They are usually partly inside the surface so you can't read them. If  
it is for a figure, you can put labels anywhere you want with "2D  
Labels" (under Tools... Utilities), but those do not move when you  
rotate the structure.  Also, there are pop-ups that say what is under  
your mouse, but they only show the detailed information when you are  
not showing the surface.  Sometimes I like to use color-coding, a  
different color for each amino acid type.  Of course, you can't have  
that as the same time as the lipophilicity or electrostatic coloring.

There is a command file (rescol.com) linked to the User's Guide that  
does my favorite residue color-coding:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile 
 >
You would save that file to your computer as plain text and just open  
it (file named *.com) in Chimera to apply the residue color-coding.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco