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
<contacts_circos.svg>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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
Hi Pete, Thanks for the quick response and for subscribing to the list to help troubleshoot this. To clarify my earlier message, I am not referring to the manual annotations. Instead, I am looking for a way to automatically display single amino acid labels with residue positions for all the partner proteins within a protein complex for e.g. peptide-MHC or peptide-MHC/β2m complexes. My goal is to create a single, comprehensive figure that allows for the comparison of interfaces across various alleles, much like the AlphaBridge diagrams shown in Figure 2A of the attached AlphaBridge paper. I have used the latest CircosContacts plugin version 0.4.8 in pursuit to create publication-quality figures for multi-interface protein complexes, such as peptide-MHC/β2m complexes. These Circos-style visualizations are incredibly informative for summarizing and comparing interfacial residues across multiple protein interaction surfaces. While the hover-over annotations in the HTML file are helpful for exploration, they do not appear in the exported .svg file. For a final publication figure, having those residue and positional labels is essential. I look forward to your thoughts on whether this level of automated labelling can be supported in the SVG export. 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 ________________________________ From: pete carlton via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 02 April 2026 12:20 AM To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: Issue with SVG export in CircosContacts plugin: Interface residues missing ! 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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Arun, OK, I think I see; your email subject "Issue with…" made me think you were reporting a bug but this seems more like a feature request, is that right? I am not entirely clear yet on what you're asking for: does "single amino acid labels with residue positions for all the partner proteins" mean you want to have a residue+number shown for every displayed contact arc? I think this could certainly be done, although it could get pretty dense with models that have many contacts, making layout challenging especially at low threshold levels. Alphabridge seems to automatically find regions with many contacts; maybe something similar where each contacting region is shown, where the actually contacting residues are highlighted? If you could give me a mockup of what you wanted to see on your previous attachment (even writing by hand a few labels and snapping a photo) it would help me envision what you are asking for. Thanks, Pete On 2026-04-03 at 19:51, arun.gupta@immonc.ox.ac.uk wrote:
Hi Pete, Thanks for the quick response and for subscribing to the list to help troubleshoot this. To clarify my earlier message, I am not referring to the manual annotations. Instead, I am looking for a way to automatically display *single amino acid labels with residue positions* for all the partner proteins within a protein complex for e.g. peptide-MHC or peptide-MHC/β2m complexes. My goal is to create a single, comprehensive figure that allows for the comparison of interfaces across various alleles, much like the *AlphaBridge diagrams* shown in *Figure 2A *of the attached AlphaBridge paper. I have used the latest *CircosContacts plugin version 0.4.8* in pursuit to create publication-quality figures for multi-interface protein complexes, such as peptide-MHC/β2m complexes. These Circos-style visualizations are incredibly informative for summarizing and comparing interfacial residues across multiple protein interaction surfaces. While the hover-over annotations in the HTML file are helpful for exploration, they do not appear in the exported .svg file. For a final publication figure, having those residue and positional labels is essential. I look forward to your thoughts on whether this level of automated labelling can be supported in the SVG export. 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
*From:* pete carlton via ChimeraX-users <chimerax-users@cgl.ucsf.edu> *Sent:* 02 April 2026 12:20 AM *To:* chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> *Subject:* [chimerax-users] Re: Issue with SVG export in CircosContacts plugin: Interface residues missing !
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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ Attachments: * AlphaBridge.pdf
participants (4)
-
Arun Gupta -
Eric Pettersen -
Peter Carlton -
pmcarlton＠carltonlab.org