ChimeraX Developer Meeting

Attendance: Tom, Zach, Eric, Greg

July 6, 2026

Agenda

• Use prebuilt Astral Python
• Update to numpy 2.
• Update to Python 3.14 (blocked by #20335 and #16848)
• Update to PySide 6.11.1
• Make Chimera 1.20 release with Mac fix.
• Inside ribbon color?
• Toolshed reduce query result size.
• Work in progress reports
• Make Chimera end-of-life bug report and registration changes.

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Discussion

• Use prebuilt Astral Python
  • Zach will switch to prebuilt Astral Python for ChimeraX daily build on Mac and Windows.
  • We will still compile Python on Linux to use system OpenSSL.

• Update to numpy 2
  • Tom will update daily build to use numpy 2 today.
  • Tom tested all major ChimeraX numpy code with numpy 2.
  • Fixed 20 file readers, 5 file writers.
  • Most problems were removed numpy function fromstring, tostring.
  • Some casting problems (16-bit integer overflows), long long default integer arrays on Windows.

• Update to Python 3.14 (blocked by #20335 and #16848)
  • Boltz does not work with Python 3.14.
  • Tom will either make it work with Python 3.14 or make it use its own Python installation.
  • After Boltz fix we can try updating daily build to Python 3.14.

• Update to PySide 6.11.1
  • Zach switched daily build from PyQt to PySide last week in daily build to work around main window resize bug with floating tools.
  • So far no PySide specific bugs reported.

• Make Chimera 1.20 release with Mac fix.
  • Greg made Chimera 1.20 release with new Tcl/Tk/Tix that fixed Mac graphics window layout bug.

• Nightly build email
  • Last few days nightly build email says all builds failed, but clicking github links says they worked.
  • Zach will look at what is going on.

• Mac Chimera nightly build failed
  • Apple updated terms of service.
  • Eric notified UCSF Apple signing certificate people who agreed to new terms.
  • Mac signing should be back to working now.

• Recent toolshed submissions
  • Tom reviewed Kurwenal toolshed submission, utilities for AI Model Angelo models built in cryoEM maps. Asked that they use normal model specs and keywords in commands.
  • Tom reviewing toolshed CryoZeta AI model building in cryoEM map, ChimeraX interface to server.
  • Zach will review carbvis toolshed submission from last week on carbohydrate depictions.

• Dockerhub ChimeraX Linux build image
  • Greg suggests putting a ChimeraX Linux build environment image on Dockerhub.
  • Tristan can use this to make a singularity image for his ISOLDE builds.

• Trajectory RMSD maps
  • Eric working on all-by-all trajectory RMSD plot tool.

• Proofpoint spamming Trac bug reports
  • Eric filed bug report about ProofPoint sending blocked email digests to Trac.
  • Frequent digests create spurious bug reports.
  • Greg notes that email2trac has a blocklist file. Made file writable by chimdev group so Eric can filter out proofpoint digests.

• Trac migration off CGL email server
  • Greg has explored how to run Trac bug reporting email2trac using rbvi.org instead of cgl.ucsf.edu.

• Group meeting topic
  • Greg presenting group meeting on Thursday.
  • Possible topic is new features in Python 3.14.

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Action Items