= 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 =