ChimeraX Developer Meeting

Attendance: Zach, Tom, Eric

April 1, 2024

Agenda

• Work in progress reports
• Update prereqs - most done.
• What ChimeraX 1.8 work/tickets should we prioritize for January?
• Worm ribbon implementation, ticket #9942
• Log slow to update when it gets long, Tristan ticket #9909
• Create Grafana dashboards to monitor web services.
• Make Chimera end-of-life bug report and registration changes for 1.18 release in Spring 2024.
• Back up the Chimera build machine to a solid state drive, Windows 7.
• ChimeraX Ideas milestone clean-up.

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Discussion

• ChimeraX builds
  • Build email is saying "Host key verification failed. fatal: Could not read from remote repository."
  • Not clear if this is fetching chimerax source or build tools from github or something the Linux singularity build is doing.
  • Greg can investigate later this week.

• Recap of last week's NIAID meeting
  • GLTF hierarchy
  • Lights in GLTF, bad colors when embedded in PowerPoint or Microsoft Word.
  • AlphaFold models in NIH 3D, what styles to output.
  • Vision Pro avatar demo from Andi, creepy.

• Alphafold prediction broke
  • Google Colab web page change broke sequence being sent by ChimeraX to Colab virtual machine.
  • Fixed but requires ChimeraX daily build.

• python_instances_of_class crashes
  • New ChimeraX crash resulting from garbage collection crash fix.
  • Eric has 200 line command script that reproduces it.
  • Involves sequences and sequence viewer must be shown.

• Volume raytracing
  • Zach says initial volume raytracing attempt too slow for interactive use.
  • Investigating how to speed it up.
  • Loic Royer wrote fast volume raytracer years ago, possibly called ClearVolume. Might also be in Napari.

• Mac Intel build failure
  • Fails creating Info.plist because of new PDB-Redo fetch.
  • Error says mtz file format does not exist.
  • Fetch of mtz needs Clipper bundle from toolshed but during build the toolshed cache has not been loaded.
  • Eric looking into solutions.

• measure contactArea command
  • Chimera measure contactArea command not in ChimeraX and needed to make Chimera image gallery binding site image.
  • Krishnan from Biocryst asked about this in ChimeraX.
  • Tom may port the contact area command to ChimeraX.

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Action Items