ChimeraX Developer Meeting

Attendance: Greg, Zach, Tom, Eric

February 12, 2024

Agenda

• Work in progress reports
• Update Cython and other prereqs.
• 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

• Update ChimeraX dependencies
  • Reviewed weekly email of PyPi dependencies that have newer versions.
  • 2/3 have already been update to latest versions.
  • Assigned who will update remaining ones.
  • Still waiting for Qt 6.6.2 to be released (was supposed to happen last week). Then we update qt 6.3 to 6.6.2.

• ChimeraX PyPi package updates
  • Decided we could do ChimeraX PyPi package update for each production release.
  • Decided PyPi package does not need to be built every night.
  • Next step is to provide Linux and Windows versions of PyPi package.
  • Use ChimeraX 1.7.1 code.
  • Also update Mac package which is from Oct 2023.

• Tom work in progress
  • Did alphafold batch protein-protein interaction group meeting last week.
  • Working on whether AlphaFold / ColabFold can run fast enough on Mac CPU.
  • Trying to understand simple ColabFold optimizations that got 5x speed-up.

• Eric work in progress
  • Debugging garbage collection crash. Have reproducible test case, but still no clear way to find cause.
  • Adding build structure gui for joining with non-peptide bonds, choosing dihedral atoms to use.
  • Looking at suboptimal idatm types for ring systems, double vs single bonds, for SPICE database molecules.

• Greg work in progress
  • Getting flatpak nightly build going. Added flatpak support to current linux build configuration files.
  • Looking at reading binary mmcif. PDB is dropping mmtf. Binary mmcif uses msgpack and does table column-wise compression. Used mostly for fast network transmission to molstar javascript in browser. May benefit ChimeraX speed if RCSB drops stylized mmcif which we rely on for speed.

• Zach work in progress
  • Exploring speech input for chimerax vr.
  • Sensitive to having a high quality microphone.
  • Want to demonstrate speech next week during NIH visit. Simple demo with flaws is fine for NIAID collaborators.

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Action Items