ChimeraX Developer Meeting

Attendance: Zach, Eric, Tom, Greg

April 13, 2026

Agenda

• macOS 27 is last support Intel apps
• Switch from PySide to PyQt.
• Progress on DockerHub ChimeraX.
• Inside ribbon color?
• Toolshed reduce query result size.
• ​Residue notes in mmCIF, Oliver Clarke
• Chimera not working with macOS 26, graphics pane positioned over command-line.
• Work in progress reports
• Make Chimera end-of-life bug report and registration changes.

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Discussion

• macOS 27 is last support Intel apps
  • Chimera won't work with macOS 28 (Fall 2027), 1.5 years from now.
  • It would probably be difficult to compile Chimera for Mac ARM since its Python packages predate Apple Silicon.
  • Users of older macOS will still be able to use Chimera, but new Macs or ones that are updated to macOS 28 will have to migrate to ChimeraX.
  • At some point after macOS 28 it may be difficult to build the Intel ChimeraX if Apple discontinues support for compiling to Intel.

• CamTools bundle review
  • Zach says CamTools bundle duplicates lots of the lighting GUI, but has a few unique features.
  • Zach will tell the developer about the lighting GUI which is only in the daily build.
  • If they want to include their alternative GUI he will approve it.

• Switch from PySide to PyQt.
  • Zach switched the daily build to PyQt last week.
  • So far no unusual PyQt bugs have been reported.
  • Plan is to distribute ChimeraX 1.12 with PyQt.

• Progress on DockerHub ChimeraX.
  • Zach has ChimeraX compiling for Docker.
  • Will make a DockerHub image by next Monday's ChimeraX meeting.

• ​Residue notes in mmCIF, Oliver Clarke
  • Oliver Clarke made a ChimeraX GUI to create and save residue notes in mmCIF files.
  • His code is on github with installation instructions.
  • Oliver originally asked if we would include this feature in the ChimeraX distribution.
  • Tom will suggest he distribute his GUI on Toolshed instead.

• Coding potholes
  • Tom described spending 3 hours debugging an off by one pixel error in QGraphicsView for mutation heatmaps.
  • Eric described spending days to track down an unsigned int comparison to -1 that broke. the ported C++ match align code.

• Mutation heatmap command
  • Discussed how a mutation heatmap command can refer to different heatmap plots.
  • Eric says sequence alignment ids are associated with the alignment data, not with the alignment GUI.
  • User is likely to want several heatmap plots with different visualization settings (colormaps, residue choices, mutation scores choice...).
  • Command should probably be able to control those heatmap visualizations by naming the plots which is a new mechanism not used with other ChimeraX data.

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Action Items