Attendees

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

June 22, 2023

Agenda

• Scooter, 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

• Download maps for Chimera
  • Greg will investigate porting Chimera usage world maps to ChimeraX (download, registration, web service, toolshed).
  • Download, registration, web service world maps were auto-generated for Chimera, broken by plato update to python 3.
  • Uses geoIP PyPi package and javascript.

• Sendmail problems
  • Sendmail problems sending cgl email after plato update.
  • Scooter thinks sendmail starts before beegfs mounted and so can't access new certificates on beegfs.
  • Restarting sendmail seems to have fixed it.
  • Plan is to move certificates off beegfs to local disk.

• Plato operating system update
  • Crick has been updated to Rocky 8, not all services tested.
  • Toolshed, SPOKE build, SFLD working on crick.
  • plato-backup still needs to be updated to Rocky 8.
  • Redhat announced yesterday plan to restrict source code access which may effect Rocky, Alma and other Linux distros.

• ChimeraX paper in Protein Science
  • Made outline focussed on model building tools.
  • Scooter created google doc, contents copied here.

Deadline: July 31
ISOLDE Paper in the same issue
Have a cross-over

E.g. Atom typing

Main themes: 
  Model Building
  Important third party bundles/extensibility

Key features to discuss:
  Alphafold/ESMFold
  Phenix
  ISOLDE

Standard workflow for unknown structure:
  Cryo-EM
  Alphafold/modeller
  ChimeraX fitting
  Phenix
  ISOLDE

Bundles:
  SEQROW
  XMAS
  StarMap
  ARTIAX
  StrudelScore/QScore
  ISOLDE

ChimeraX Tools:
  De novo building
    AddH
    Pubchem fetch
    Smiles fetch
    IUPAC fetch
    Peptides and nucleotides
  Rotamers
  Alphafold
  Phenix bundle
  ESMfold
  Modeller
    Comparative
    loops
  AddCharge
  DockPrep
  VR/Standalone VR

Action Items

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