Begin forwarded message:
From: Ratchanont Viriyakitkosol <ratchanont.vir@gmail.com> Subject: Request for Help with Chimerax and Protein Visualization Date: March 2, 2023 at 12:26:42 AM PST To: pett@cgl.ucsf.edu
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