= 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 =