[chimerax-users] contacts and disulfide bonds

[Elaine Meng]

Dear James,
Please use the chimerax-users at cgl.ucsf.edu address to ask ChimeraX questions.

(1) Regarding your question about "contacts" it was just answered on that mailing list, see:

(2) Regarding disulfide bonds:  ChimeraX just shows the covalent bonds that are already defined in the input file, including any disulfide bonds.  It doesn't have a tool to specifically predict disulfide bonds between two -SH groups that are close together but that didn't have a bond according to the input file. 

If disulfide bonds are not defined in the input file, one thing you can do is to highlight all cysteine residues and try to judge for yourself (by looking at where they are in the structure) if any pairs of them might form a disulfide bond.  E.g. commands:

hide atoms
show :cys

If disulfide bonds are already defined in the input file you can select/highlight them, e.g.:

show :cys
select disulfide

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

> On Mar 2, 2023, at 7:22 AM, Eric Pettersen via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
>> Begin forwarded message:
>> 
>> From: Ratchanont Viriyakitkosol <ratchanont.vir at gmail.com>
>> Subject: Request for Help with Chimerax and Protein Visualization
>> Date: March 2, 2023 at 12:26:42 AM PST
>> 
>> Dear Eric Pettersen,
>> 
>> I hope this email finds you well. I am a medical school undergraduate student, and I have been using Chimerax to visualize protein structures that I predicted using AlphaFold. I am reaching out to you as I have encountered some difficulties with visualizing chemical bonding interactions in Chimerax, and I was hoping you could provide some guidance.
>> 
>> Firstly, I have been using the "contacts" command in Chimerax to visualize chemical bonding interactions that interact with a single amino acid. However, I am not sure if this is the correct command to use. The visualization only shows blue dashlines, which I assume are hydrogen bonds. However, I am not sure if it is showing all direct interactions, including polar and nonpolar, favorable and unfavorable (including clashes). I want to know what is meant by "favorable and unfavorable" interactions in this context.
>> 
>> Secondly, I have been unable to find a command to show disulfide bonds within a protein in Chimerax. I know that Pymol can show disulfide bonds in the same model, but I find Chimerax easier to use. Could you please let me know how to visualize disulfide bonds in Chimerax?
>> 
>> As an undergraduate student with limited knowledge of structural analysis, I want to ensure that the bonding I use in my manuscript is shown correctly. I would greatly appreciate any advice or guidance you could provide.
>> 
>> Thank you for taking the time to read my email, and I look forward to your reply.
>> Best regards,
>> 
>> James