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