Attendees

Selina, Zach, TomG, Eric, Elaine, Greg, Scooter, TomF

June 29, 2023

Agenda

• Discussion of ChimeraX manuscript for Protein Science, due July 31, 2023
• ProofPoint email filtering interaction with ChimeraX bug reports and mailing list.
• New hardware
• Review Action Items listed below

Discussion Notes

• ProofPoint email filtering
  • UCSF IT insists we enable URL mangling using urldefense.com for incoming emails.
  • Scooter thinks this is bad for the ChimeraX mailing list and Trac.
  • Suggests we implement ProofPoint and ask for a 1 year excemption from urldefense.
  • Another problem with url mangling is it breaks DKIM mail signatures. There is an option to not mangle DKIM signed emails but we don't have that option in our ProofPoint sub-console.
  • Might be possible to white-list sites to avoid url mangling, but Scooter did not see that option to white-list based on the "To" header, only the "From" header.

• Elaine's ​cryoEM workflow examples

• Outline for ChimeraX paper
  • Made outline in Google Doc, copied here

Outline:
  1. Introduction
    Example Cryo-EM workflow
      Get starting structures (experimental, AlphaFold, Modeller, etc.)
      Optionally segment the map
      Fit the structures into the map
      Build and add het groups, nucleic acid chains, etc.
      Refine (phenix, Starmap, ISOLDE, etc.)
      Validation and evaluation (visualize/VR/QScore)
      Iterate as necessary
    Other model building requirements
    ChimeraX model building capabilities
    ChimeraX extensibility (third party bundles)
  2. ChimeraX role in Cryo-EM model building
  3. ChimeraX role building non-Cryo-EM structures
  4. ChimeraX Extensibility
    ChimeraX Third Party Bundles
  5. Conclusion

Action Items

• Clean up VirtualHosts on our web servers -- Greg/Scooter
• Document new vpn setup on Linux -- Scooter
• Audit followup -- Scooter