ChimeraX Developer Meeting

Attendance: Greg, Zach, Tom, Eric

January 29, 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

• Chimera Windows build
  • Build is now working after reverting cygwin gcc version.
  • But sqm is not working in the Windows Chimera because a fortran library was not copied to the build.
  • Eric added the missing library and will retest on Thursday.

• Networking problem with Elaine's new iMac
  • Not able to copy the daily build to Elaine's new iMac chopin.
  • That new machine has no ethernet jack so a dongle is used.
  • Problem was related to network access control and that there was a switch under the desk.
  • Removing the switch fixed it.

• RCSB dropping mmtf format
  • RCSB is dropping the mmtf format which we read.
  • They recommend using binary mmCIF which we do not read.
  • Greg may be interested in reading binary mmCIF in the future.

• mmCIF missing atom type field
  • Greg got bug report of mmCIF failing to read because atom table element type field missing.
  • That field is mandatory in mmCIF.
  • Eric says PDB reader has many convoluted rules to guess element type for PDB files that don't have it.
  • Decided it is not worth supporting mmCIF without element type unless more people complain.
  • Greg told user that the software writing the file should be fixed.

• Labeling tiled models
  • Tom wanted labels below 30 tiled alphafold models.
  • Uses Python script to make 2D labels.
  • 2D labels are misaligned as soon as you zoom.
  • 3D labels can only be on atoms, or residues or bonds or pseudobonds, so won't work for maps (e.g. class averages that Oliver Clarke tiles).
  • One idea is to make label command able to label a model or maybe even just label a fixed scene coordinate.

• Running AlphaFold without Google Colab
  • Tom looking for ways for users to run AlphaFold besides the limited Google Colab.
  • Needs Nvidia graphics and Linux.
  • For UCSF users, Wynton cannot run the 10x faster Colabfold because internet access to sequence server is blocked.
  • Tom Ferrin and Andrej Sali are seeing if Wynton can unblock some URLs.
  • Apple is trying to write a backend for XLA (accelerated linear algebra) to use Metal which might allow AlphaFold to run on Macs in the future. Not working in current version 0.0.5.

• Speech input in ChimeraX for VR
  • Zach has tried Whisper from OpenAI that runs locally on user's machine, has python library.
  • Scooter also suggests comparing to a Google speech to text service that also has a python library.

• Selina's medical image tumor segmentation in ChimeraX
  • Zach showed Selina how to get best rendering of images in ChimeraX.
  • Zach working on ChimeraX web service backend support to use qsub on Wynton to submit jobs and monitor when the finish.

• Email to Trac
  • Greg and Eric working to fix trac database.
  • Eric had to hand resubmit 20 bug reports arriving over the weekend because trac was down.
  • Greg rebuilt database, also needed to clean up temporary table listing pending ticket number.
  • Greg says there is a README file in /usr/local/share/Trac on plato describing how to fix Trac.
  • Requires root to rebuild Trac.
  • Greg suggested making a script to do it so any of us could sudo to restore database.

• Combine chains
  • Eric improving combine command to merge two chains with same id into a single chain.
  • Currently it only is able to make two chains.
  • Still working with fixing up the merged chain sequence information.

• SPICE database idatm types
  • Eric working on getting idatm types for SPICE database molecules.
  • SPICE molecules are in hdf and need custom code to read into ChimeraX.
  • Main problems now are idatm types that disagree with protonation state of database molecules.

• Email DKIM support
  • Greg plans on making plato outgoing email sign with DKIM.
  • This prevents sending plato email from unauthorized servers.

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Action Items