= 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.

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

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