ChimeraX Developer Meeting

Attendance: Zach, Greg, Piet, Tom, Eric

January 27, 2025

Agenda

• Possible updates Python 3.13, numpy 2, PySide6
• 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.

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Discussion

• N453 door lock
  • The N453 door keypad lock needs to have the code set to allow keeping door unlocked all day.
  • Greg will call to have this done. Greg has chart string for payment.

• Plato home directory changes
  • Greg, Tom Ferrin and Scooter discussed plato home directory changes last week.
  • Goal is to remove from plato all wynton PHI or root management access so that plato is only at P1/P2 security level instead of P3.
  • Plato will use shadow home directories on NAS that can symbolic link either to a NAS home directory or NFS mounted wynton home directory.
  • Login to log1.wynton.ucsf.edu will always give Wynton home directory (on beegfs).
  • Wynton LDAP and Kerberos authentication servers are still on plato. UCSF IT is working on a centralized password management and have chosen a vendor that will replace current LDAP/Kerberos.

• Web update failures
  • Nightly webpush sometimes fails with emailed traceback saying a directory could not be deleted because it was not empty.
  • Eric says this usually involves corrective action like another webpush or pcs restart to restart web service.
  • Greg will look into why. Says this happens more often with web site on NAS, but used to happen on BeeGFS sometimes.
  • Problem happens more often with Chimera web site, less often with ChimeraX web site.
  • Elaine and TomG notice updating web site files sometimes the fails to show them on web page for 30-60 seconds.

• Qt 6.8.2 update
  • Qt 6.8.2 is not out yet. Was planned to release Jan 23. Often they are 1-2 weeks late.
  • We will update ChimeraX from 6.7 when 6.8.2 comes out.
  • 6.8.1 had crash on exit on Mac, supposedly fixed in 6.8.2.
  • Hope is that 6.8 might fix Mac multi-display crashes.

• PySide 6, Python 3.13, Numpy 2 updates
  • TomG suggests with grant renewal activities in the next 5 months we probably should try updating these major packages since there will not be time to fix all the problems.

• Faster atom specifier parser
  • Eric says almost ready to try C++ faster atom spec parser.
  • There will be an option to enable it during a testing phase.
  • Bugs are expected.

• AlphaFold 3 clones
  • Tom is looking at Chai-1 and Boltz-1 clones of Alphafold 3.
  • They have more open license terms.
  • They may support newer features than AlphaFold 3 such as specifying where ligands or antibodies should bind or using experimental structures as parts of complexes.

• Scooter
  • Scooter meeting with UCSF HR tomorrow to discuss his leave.
  • HR said a week ago they didn't know anything, but will investigate and report tomorrow.

• Endowed chair search committee
  • Tom Ferrin reports that the endowed chair search committee has been formed.

• Speed up sequence conservation
  • Eric made computing sequence conservation for 50,000 sequences 100x faster.
  • Was taking 3 minutes because every character lookup was done by C++ copying the entire sequence.
  • This is for use with new Profile Grid sequence viewer.

• Piet scene progress
  • Piet will report on scene API progress Feb 13 at group meeting, also Elaine presenting that day.

• ScholAR
  • Piet has not heard back from Tyler from USC about ScholAR improvements so Piet is currently not working on that.

• ViewDockX
  • Piet is looking for next project, Eric suggests porting ViewDockX from html/javascript to Qt.
  • Tom says Brian Schoichet and John Irwin labs still using Chimera ViewDock due to poor function of ViewDockX.
  • Eric and Elaine will write-up what improvements are needed in the ported ViewDockX and give that to Piet to consider.

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Action Items

• Greg will get N453 keypad able to unlock all day by contacting building maintenance.