[Chimera-users] identifying residues in a surface
meng at cgl.ucsf.edu
Tue Dec 22 10:16:39 PST 2009
On Dec 21, 2009, at 5:14 PM, gytjyb wrote:
> 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!
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
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:
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 C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
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