= 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.

--------------------------
= 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.

--------------------------
= Action Items =

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