ChimeraX Developer Meeting

Attendance: Greg, Zach, Tom, Eric

February 26, 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

• NIH visit
  • Ribbon worms added to NIAID statement of work.
  • Pass-through VR video for ChimeraX added to SOW.
  • Wall touch screen had very wide 3:1 aspect not ideal for ChimeraX, but having tools on both left and right side helped. Command-line in side panel helped prevent it from being hidden by Windows task bar at bottom of screen.
  • Discussed ThinLinc virtual machine service at NIAID that allows using ChimeraX via web browser linux remote desktop. Had Nvidia A100 80 GB GPU!

• ChimeraX 1.8 roadmap
  • NIAID wants worm depiction.
  • NIAID wants ChimeraX VR pass-through video using OpenXR.
  • Greg would like to use generic Python 3 C API so ChimeraX module can run in Python 3.11 and newer instead of just 3.11.
  • Greg would like to allow ChimeraX flatpak linux distribution to use system Python 3.11.

• Large log fix
  • Eric has idea to fix the slow Log panel update when Log gets very large (> 1 Mbyte).
  • Could not embed previous session logs in the current log and instead use a special internal url scheme that brings up those older session logs.
  • Would display in a separate log panel.

• Eric work in progress
  • Added join models with non-peptide bonds.
  • Made table widget able to save comma-separated values file.
  • Finished SPICE database idatm typing. Next Tristan's people will train neural net to produce OpenMM parameterization.
  • Have 30 garbage collection crashes in 1.7 reported. Have simple dipeptide + coulombic + close + garbage collection test case that crashes. Appears to be related to chains or sequences since pubchem molecules don't crash. Still trying to locate code that causes crash.
  • Starting ChimeraX with 2 screens in windows when last chimerax size was large can lead to frozen, unmovable ChimeraX. Debugged and put in work-arounds for this.
  • Updated Mac to AmberTools23 yesterday. Library loader paths wrong so not working in daily build, also broke Mac notarization. Will revert today to AmberTools20 until loader paths can be fixed.

• Tom work in progress
  • Will test vmtouch to keep sequence databases in memory on crick for multiple sequence alignment server.
  • Need to fix meeting bug in LookSee VR with hand tracking.
  • Discussing biology projects with a few NIAID researchers.

• Greg work in progress
  • Recovering bad blocks on wynton beegfs that resulted from last year's disk failures. Will allow reusing spacing and not count toward user disk quota.
  • Wynton may add visualization nodes where user could run ChimeraX on wynton to view data on wynton without copying data to local machine for visualization.
  • Will try updating pip in ChimeraX.

• Zach work in progress
  • Small group of 5 at medical imaging tutorial at NIAID, good discussions.
  • One user interested in spatial genomics visualization. Hope to get data from them.
  • At NIAID discussed putting ChimeraX medical imaging into a bundle and also providing separate ChimeraX UI tailored to medical imaging.
  • Will update medical imaging prereqs.

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Action Items