Attendees

Scooter, Eric, Tom Goddard, Greg, Elaine, Tom Ferrin

September 11, 2025

Agenda

• Eric, work in progress
• Phenix R24 grant renewal due September 25
• What to do with unused Cytoscape GPU nodes

Discussion Notes

• Windows installer signing
  • Tom Ferrin gave Greg the yubi key needed for Windows code signing.
  • Greg will try to get it to work without having to be touched so nightly builds can be signed again.

• Wynton move
  • Scan of wynton file system to find old-unused files by Starfish has not been done yet.
  • Purpose is to see what data needs backup for moving Wynton to co-location facility.

• Phenix R24 grant renewal
  • Tom Ferrin has completed forms for Phenix R24 subcontract. One sent back for revision that he is working on.

• Fit ligands Phenix tool
  • Eric demonstrated fit ligands ChimeraX gui that calls Phenix.
  • Failed to find fit on Mac laptop. Worked an hour earlier in Phenix meeting on Mac desktop.
  • Second run appeared to work but was missing most of atoms of the BER ligand, and placed it outside of cropped map. Could be bug in newer Phenix installed on laptop.

• OpenMM minimization
  • Can be done in daily builds with Langevin step routine which can move atoms further than user might want (e.g. ions move to different site).
  • Steepest descent and conjugate gradient are in another OpenMM-Tools package on Conda. Installing that requires other dependencies.

• ViewDock
  • Eric made gui improvements to ViewDock so column checkbuttons and description don't expand dialog too much.

• Scenes
  • Improving scene code organization so each Model or derived class defines how to save and restore scenes.

• CryoEM workshop Boltz talk
  • Tom Goddard gave 60 minute Boltz talk plus 45 minutes of Q&A at Pacific Northwest cryoEM Center workshop.
  • Video will be put online and we can link to it from our videos page, or BlueSky, and outreach events page.

• Web site accessibility compliance
  • Greg is trying to get access to web site accessibility test tools used by UCSF.

• Licensing email
  • Greg changed the chimera licensing email address to a mailing list so the messages are now archived.
  • Elaine made a mailman account so she can see the archive and explained how to get access to department licensing people.

Action Items