[Chimera-users] Chimera Color Coding Chains that are Interacting

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 1 09:46:39 PST 2018


Hi Andrew,
I’m not understanding exactly which interactions you are trying to find and what you want to color. Simply definining the problem more precisely should clarify what steps are needed.

Which interactions: you said “intramolecular bonds within a complex” … do you mean you want to identify the atoms involved in the interface between two chains?  Are there more than two chains in the complex?

What to color: you said “color coding chains” … do you really mean coloring each whole chain the same color, or just the atoms in the chain that are involved in some interaction?

There is a tutorial on coloring the atoms (and their surface patches) involved in a chain-chain interface here, but I really can’t tell if that’s what you want to do…
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>

Alternatively, especially if this is a very large complex with multiple chains, you might be interested in our next-gen program ChimeraX (like Chimera, free download for noncommercial use), and its “interface” command for analyzing chain-chain interfaces:
<http://www.rbvi.ucsf.edu/chimerax/index.html>
<http://www.rbvi.ucsf.edu/chimerax/features.html#chain-network>
<http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>

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

> On Jan 31, 2018, at 3:19 PM, Andrew Cuyegkeng <ajcuyegkeng at ucdavis.edu> wrote:
> 
> Hello,
> I am an undergraduate researcher still learning how to use Chimera. Our lab is exploring intramolecular bonds within a complex. I am aware of the FindContact tool but was running into problems when it came to color coding these interactions. I would like to color code the different chains that are involved in these interactions and make everything that's not interacting the color black. What would the best approach to this be?
> Thanks,
> Andrew




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