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

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 1 13:43:42 PST 2018

Hi Andrew,
As David said, 
(1) color everything black.

(2) select interface atoms:
Then it sounds like you may want to use Find Clashes/Contacts multiple times, each time specifying to look for interactions between two sets of atoms, one chain vs. another chain, and using the option to “Select” the contact atoms. (Do not use the option to “Color” since you don’t want to make them all the same color.)

...or instead of the Find Clashes/Contacts dialog, you could use the “findclash” command with the corresponding options, for example between protein parts of chains B and C with something like:

findclash :.B&protein test :.C&protein overlap -0.4 hb 0 make false select true

(or whatever parameter values you were using in the dialog)

(3) color the selection:
After each findclash, you would then have a set of selected atoms, those in the interface between two chains.   If you want to color whole residues, not just atoms (which could be fragments of residues), enter command “select up” to promote the selection to whole residues.  Then, color the selection, but a different color per chain.  For example, if you’d identified contacts between chains B and C, the coloring commands could be something like:

color hot pink sel & :.B
color orange sel & :.C

Then you’d go back to finding the contact atoms for another pair of chains, coloring them, etc. etc. 

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

> On Feb 1, 2018, at 12:52 PM, David Gae <ddgae at ucdavis.edu> wrote:
> Dear Andrew,
> In addition to what Dr. Meng suggested in the previous email. I think this tutorial link may help you http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html 
> For example:
> color black :*   (will color everything black)
> color red :100  (will color amino acid 100 positions red) 
> color blue :500.c (will only color chain C amino acid 500 position blue)
> I hope this helps, 
> David 
>> On Feb 1, 2018, at 11:09 AM, Andrew Cuyegkeng <ajcuyegkeng at ucdavis.edu> wrote:
>> Hello again,
>> Sorry for the very vague email.
>> The protein complex I am looking at has 8 different chains. I want to identify the atoms/residues involved in the interface between two chains and color code the residues involved based on what chain they are on. For example, if we had the following points of contact:
>> Tyr 100.A    <----> Asp 500.C
>> Lys 200.A  <---> Leu 400.D
>> How can I color the Tyr 100.A and Lys 200.A the same color (since they are on the same chain), and Asp and Leu both different colors? And then how can I make all residues   not involved in the interface the same color (like black)? I just want to make all interacting residues on the same chain the same color, and everything that is not interacting the color black.
>> I hope this clarifies things! I apologize: I just started using the program last week and have gone through the online tutorials, but I'm still unfamiliar with the majority of the tools/commands.
>> Best,
>> Andrew

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