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

David Gae ddgae at ucdavis.edu
Thu Feb 1 12:52:16 PST 2018


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 <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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