ChimeraX Developer Meeting

Attendance: Greg, Zach, Tom, Eric

August 11, 2025

Agenda

• Spiffy C++ features
• Updating prereqs.
• Switch from PyQt to PySide?
• ViewDockX port to Qt
• Inside ribbon color?
• Work in progress reports
• Make Chimera end-of-life bug report and registration changes.
• Back up the Chimera build machine to a solid state drive, Windows 7.
• Linux ARM64 release and download page

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Discussion

• Pip install of kvFinder fails on Windows sometimes
  • Eric not able to reproduce this.
  • Apparently exit code is non-zero but the pip error log is empty.

• Windows ChimeraX installer signing
  • Greg still studying yubi key and signing certificate from UCSF.
  • Discussed Azure Cloud signing, $10 per month, requires identify verification including business documentation and 3-year tax history info.
  • No good solution apparent.
  • Tried unsigned Windows daily build on download page during meeting. Relatively easy to install after clicking "More Info..." when given unverified warning, may damage your computer. Starting ChimeraX gives no warnings after installed.
  • We will provide unsigned Windows builds until we get installer signing working again.

• ViewDock improvements
  • Eric is improving layout of ViewDock attributes, less white space.
  • Elaine provided Maestro Glide example data that had 70 attributes per ligand. This made dialog very wide due to 8 by 8 grid of column checkbuttons. Eric will make it narrower. May make attribute value panel scroll.

• chirality command added
  • Eric added a mostly working chirality command that reports for an atom if it is non-chiral or R or S chirality.
  • Some devilish cases are not handled that depend on bond order that ChimeraX does not know (code guesses), and when tie breaking using side group stereo-center handedness.

• Boltz ligand predictions
  • Tom read article that showed ligand predictions of AF3, Boltz and others are mostly just memorized training data. Accuracy is proportional to how many times similar ligand and pocket seen in training data.
  • Tom has batch ligand predictions working in a ChimeraX branch, probably will release this week or next.

• PNNL cryoEM workshop
  • Tom giving 90 minute ChimeraX tutorial via Zoom on Sept 4 for workshop organized by Omar Davulcu.
  • Will present ML structure prediction.

• Update prereqs
  • Time to update prereq packages for ChimeraX 1.11.
  • PyQt already updated to Qt 6.9.1.

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Action Items