= ChimeraX Developer Meeting =

Attendance: Greg, Zach, Tom, Eric

February 26, 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.

--------------------------
= 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.

* 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.

* 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.

  
--------------------------
= Action Items =