ChimeraX Developer Meeting

Attendance: Zach, Eric, Tom, Greg

March 23, 2026

Agenda

• PySide, any new bugs?
• Toolshed reduce query result size.
• Chimera not working with macOS 26, graphics pane positioned over command-line.
• Work in progress reports
• Inside ribbon color?
• Make Chimera end-of-life bug report and registration changes.

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Discussion

• Plato admin
  • Greg considering moving password expiration script from wynton back to plato.
  • Announcement that wynton passwords expired was a mistake, was using old kerberos database. Greg will send out a correction.

• PDB database updates
  • Eric did not receive email last weekend about PDB database on plato updating.
  • Will wait to see if update works next weekend.

• PySide bugs
  • There are two frequently reported PySide crashes. If we release with these in June we could get a large number of crash reports.
  • We will try PySide 6.10.3 when it comes out in the next week.
  • PySide 6.11 is out today, but too late in our release cycle to update to that.
  • Crash during garbage collection deleting a QDockWidget, often from DockPrep.
  • Crash in Qt setParentChanged() where it appears ChimeraX is exiting normally in Py_FinalizeEx() and atexit_callfuncs(). But Elaine hit this crash and she was not quitting, was changing Mac scrollbar auto display setting.

• OpenFold and AlphaFold
  • Tom trying latest OpenFold preview 2 released a week ago. Reran antiviral ligand geometry tests. Small improvement.
  • Running AlphaFold 3 latest github code to try 7000 amino acid pooled predictions for Horia Todor on RunPod.
  • Latest AlphaFold 3 did not improve ligand geometry problems versus original Nov 2024 AlphaFold 3.

• Jane Richardson Phenix talk
  • Jane talked about two projects she will continue work on after June retirement.
  • Figuring out RNA base geometry at low resolutions.
  • Combining phi/psi ramachandran backbone angles with sidechain rotamers in determining favored geometries.

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Action Items