= ChimeraX Developer Meeting =

Attendance: Greg, Zach, Tom, Eric

April 8, 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 =

* How to handle MTZ format when Toolshed cache not initialized
  - Looked at ticket #14862 startup error caused by PDB-Redo registering MTZ fetch when Toolshed not initialized so it didn't know Clipper on Toolshed provides MTZ reading.
  - Discussed 8 possible solutions.
  - Currently Eric downgraded error to an info message.
  - Eric will reevaluate which solution is best.

* PyTables failing to read some HDF5 files
  - New pytables in daily build fails to read some EMAN HDF5 files that ChimeraX 1.7 read.
  - Tom will probably revert PyTables version.

* Cython on Mac ARM
  - Tristan had a problem where Cython not in Mac ARM builds.
  - Greg believes it is fixed, by compiling Mac ARM Cython separately, and will ask Tristan.

* Medical imaging on Toolshed
  - Zach working on putting medical imaging in Toolshed.
  - Enhancing Toolbar interface to be able to remove buttons and add buttons.
  - Will add a button to medical imaging toolbar to install from toolshed.
  - Will reconfigure Toolbars hiding molecule ones if user wants medical imaging user interface.

* Sequence alignments from structure alignments
  - Eric porting Chimera ability to make sequence alignments from structure alignments.
  - Case of two structures is easy, but more than two is very hard.
  - Working on more than 2 in C++ where it was in Python (and very slow) in Chimera.

* Klim Verba meeting tomorrow, comparing kinases
  - Tom is meeting Klim Verba and grad student tomorrow to discuss how to compare tens to hundreds of kinases.
  - Interested in seeing sequence differences and conformation differences.
  - Interested in how to locate related structures, maybe BLAST of PDB.
  - Klim's group analyzes kinase sustrate specificity.

* python_instances_of_class crash
  - Eric has fixed an often reported crash in daily build where C++ mapping from C++ object (e.g. Atom) to Python object became invalid.
  - Sequence __del__ method was not called and so pointer to freed Python objects in C++ table were not being removed.

* Replace PyQt with PySide6?
  - PyQt license needs to be renewed this month.
  - Might want to try replacing PyQt with PySide6 after ChimeraX 1.8 is released.

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= Action Items =