Issue with SVG export in CircosContacts plugin: Interface residues missing !
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
Dear Arun, The author of the CircosContacts plugin is not subscribed to the chimerax-users list. I will forward your email to him. --Eric Eric Pettersen UCSF Computer Graphics Lab
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
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Hi Arun, thanks for reporting this (and thanks to Eric for letting me know; I've subscribed to the list now). Are you talking about the annotations that appear in the html file when you hover over the protein or contact arcs, or to manual annotations you've added? Only the latter can appear in the SVG file, and I don't know what kind of annotations you may have added since they're not visible (and no trace of any annotations in the SVG file contents). Could you either provide the saved HTML file, or the PDB/mmcif or contact files, and let me know which version you used, so I can try to reproduce? Using plugin version 0.4.8, manually-added annotations are visible in my exported SVG files. -Pete
participants (3)
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Arun Gupta -
Eric Pettersen -
pmcarlton＠carltonlab.org