ChimeraX Developer Meeting

Attendance: Greg, Zach, Tom, Eric

August 25, 2025

Agenda

• Include PySide fixes in develop branch for easier testing.
• Can we use Cytoscape GPU nodes for structure prediction?
• 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

• Windows ARM installation
  • Windows installer used to allow installing Intel ChimeraX on ARM to run under emulation.
  • That ability was missing in 1.10 release from change to Github Action builds.
  • Zach has added installing on Windows ARM in daily build.
  • Appears not many Windows ARM users since ChimeraX 1.10 has been out a couple months and we just heard about the installer problem today.

• Windows installer signing
  • Tom Ferrin has ordered Yubi key for Windows ChimeraX signing.
  • Greg thinks it can be automated so no button press on yubi key is needed to sign nightly builds.
  • Expected to arrive later this week.

• PySide easier testing
  • Zach says he commits PySide fixes to both the develop and pyside branches of ChimeraX.
  • So we can easily try PySide with the develop branch when we are testing whatever we are currently working on.
  • There is a USE_PYSIDE (?) environment variable when building to get PySide instead of PyQt.
  • Alternatively PyQt can be pip uninstalled (also PyQt-WebEngine) and PySide pip installed.

• Cytoscape GPU nodes
  • Greg, Tom Ferrin and Tom Goddard looked at two GPU nodes (8 L40S GPUs) in BH-101, not currently powered.
  • Still need to find a location (N453?) with adequate power and cooling to run them.
  • Also need to see what purpose Scooter wants to put these nodes to.

• Wynton news
  • Greg says a plan for moving Wynton to CoLab off-site facility will be produced by academic research computing (Mandy) by end of September for Sam Hagwood to review.

• ViewDock
  • Eric gave improved viewdock back to Shoichet lab tester Andriy.
  • Soon will remove ViewDockX bundle.

• numpy 2
  • Discussed updating numpy 1 to numpy 2.
  • Will be needed for Python 3.13 because numpy 1 binaries are not available for 3.13.
  • Decided to wait until Spring ChimeraX release. Work on one major change, PyQt to PySide for this December release.

• Prereq updates
  • Eric unpinned prereqs to see if new ones work, then will pin new latest versions.
  • Greg has updated some prereqs. Newer Cython since update is available.
  • Tom has not made updates yet.

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Action Items