Dear ChimeraX Team,

Today I tested the CircosContacts plugin in ChimeraX to generate Circos plots for the peptide–MHC interface. The plugin works as expected in the CircosContacts HTML webpage, where I can see the interface residue/atom contact details between the peptide (Chain Id - C) and MHC chain (Chain Id- A).

However, I am not able to observe the interface residues in the exported contacts_circos.svg file. The SVG export appears to be missing the interface residue annotations that are visible in the HTML view.

I have attached the exported contacts_circos.svg file for reference. For reproducibility, I used the following command:

circoscontacts #1/A restrict #1/C outputDir /Users/arungupta/010426_contacts_1 interModel true intramol false

Could you please let me know whether this is expected behavior, or if there is a workaround to ensure that the interface residues are included in the exported SVG file as well or if this is a known limitation of the current version of the plugin ?

Thank you for your time and for developing such a useful plugin.

Best regards,

Arun

Arun Gupta PhD, MRSC