wiki:Dev2024-2-5

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.

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.

Action Items

Last modified 21 months ago Last modified on Feb 5, 2024, 4:05:45 PM
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