ChimeraX Developer Meeting

Attendance: Zach, Tom, Eric

February 5, 2024

Agenda

• Fix Chimera Windows build broken by updating cygwin.
• 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

• Windows Chimera build charge calculation
  • Eric fixed copying of fortran library to distribution.
  • Charge calculation on 2gbp worked.

• Chimera on Nvidia 4070
  • On vive.cgl.ucsf.edu Windows 10 showing only black graphics pane.
  • Replaced Quadro P6000 with Nvidia 4070 a couple weeks ago (for VR NIAID testing).
  • Chimera problem was it was using stereo mode.
  • Fixed by switching to mono camera.

• Speech to text for ChimeraX control
  • Scooter asked Zach if we can demo speech to ChimeraX commands during NIAID visit.
  • Zach trying OpenAI Whisper and a Google speech to text service.
  • Zach says you have to yell to get reliable speech to text.

• AlphaFold group meeting for John Gross lab
  • Tom giving presentation on running alphafold to find protein-protein interactions tomorrow.
  • Slides

• SPICE idatm typing
  • Eric talked to Peter Eastman about extremely unlikely protonation states in SPICE database.
  • Peter says as long as they are physically possible they are not considered a problem.
  • Eric will simply drop SPICE entries that cannot be idatm typed.
  • Will keep ones with exotic protonation.
  • Goal is to provide these idatm types to train a ML network to predict charges.

• Grafana
  • Zach says Scooter suggests running it as nightly cron job.
  • Last try to setup realtime monitoring generated lots of processes that Scooter had to kill, and Zach says all data files were erased.

• mmseqs2 sequence alignment on plato
  • Tom will try installing mmseqs2 sequence alignment for ColabFold on a plato node.
  • May use new SSD drive for databases.
  • Testing to see if ColabFold server will work with Rocky 8.
  • If it works we may get 1 Tb memory to run a ColabFold sequence server.

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Action Items