On Apr 1, 2026, at 7:33 AM, Arun Gupta via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
Sr. Post Doctoral Research Assistant
Gillespie/McMichael Group
Nuffield Dept. of Clinical Medicine,
University of Oxford,
Centre for Immuno-Oncology
Old Road Campus Research Building,
Roosevelt Drive, Oxford
OX3 7DQ