Attendees

Scooter, TomG, Selina, Greg, Zach, TomF

October 19, 2023

Agenda

• Selina presenting
• Phenix workshop at University of Kansas at Lawrence, Nov 9-10, Zach giving tutorial

Discussion Notes

• ChimeraX library license
  • Looked over LGPL license text Zach added to ChimeraX library source code files.
  • Everyone thinks it is adequate.

• CZI grant final report
  • Scooter is writing final report for CZI grant
  • Have $50K left over and Scooter will ask for no-cost extension.

• Medical imaging collaborator
  • Charlie Craik mentioned a possible UCSF radiology collaborator Mike Evans for the ChimeraX med imaging.

• Preview web site
  • Greg suggests disabling (making private?) preview web site.
  • Too much traffic, possibly due to burst of large language model training scanning the web.

• Metric Ion Classification
  • Selina presented her work with Mike Keiser's lab to classify ions in cryoEM structures.
  • Uses atomic model and optionally cryoEM map and identifies type of ion (Na, K, Mg, Zn, water, ...) at given locations.
  • Used machine learning method called metric classification.
  • Used LUNA fingerprinting of atoms in concentric shell around putative ion site as input to prediction.
  • About 80% accuracy.
  • Takes about a second per site for prediction. Typical structure might have ~400 sites, so several minutes.
  • Selina developed confidence scoring method DQD.
  • Might want to add this as a ChimeraX web service.

Action Items