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.

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
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