Attendees

Elaine, Eric, Greg, Conrad, TomG, TomF

Agenda

• Review action items from last meeting
• Chimera 1.11.1 release
• ChimeraX issues
• Meghan issues
• Assign required site-visit functionality to people
• Continuation of 8-29 discussion

Discussion

• Previous action items:
  • ChimeraX licensing
    • Click-through license for non-commercial ChimeraX is working
    • Embedded software list is included in distribution
• Chimera 1.11.1 release
  • Candidate releases are up
    • Conrad is working on builds hanging on Windows
  • Need to implement fix for blastpdb before final 1.11.1
    • Fix by replacing Opal script with shell script that displays error message and exit with status 1
    • Waiting to see "final" format for pdbaa and nr FASTA files from NCBI
• ChimeraX issues
  • Ribbon progress
    • Conrad implemented "peptide" keyword for "cartoon orient" option
    • Lots of stuff on Elaine's documentation page
    • Conrad is still working on curved (arc) strands
  • X3D export
    • Textures are not included
    • Triangle masks are honored
    • Instancing works for spheres and cylinders
    • Greg and TomG will investigate how "sym" command uses instancing
  • Investigate protein h-bonds/ss-bonds in mmCIF
  • Display DSSP h-bonds for comparison with other sources
• Meghan Chimera (not ChimeraX) issues
  • We do not have resources to make ChimeraX usable for them by November
  • Chimera 1 struts now includes all h-bonds in pseudobond group as "normal" bonds in calculation
  • TomF will inform Meghan of our decision
• Assign required site-visit functionality to people
  • Cytoscape and REST interface (Conrad, Scooter)
  • Side view on PyQt (Greg)
  • Toolshed (Conrad, Greg)
  • Ribbons (Conrad)
  • IHM cross-link distribution histograms (TomG)
  • Chain contact graph (TomG)
  • Domains
    • Web service, Uniprot? (Eric)
    • Integration into hierarchy (Eric)
    • Interactive 2D graph (team)
  • IHM mmCIF support (TBD)
  • -----
  • String database (Scooter, Conrad)
  • Hydrogen bonds and contacts (Eric)
  • MAV (Eric)
  • Link to NGL, LiteMol (Scooter, Conrad, Greg)
  • Molprobity on Opal (Scooter)
  • UI cleanup (team)
• Continuation of 8-29 discussion
  • Conrad presented Scooter's vision of UI (took an extra hour)
  • Split "Assembly" into top-level "Data source" and "assembly"
  • TomG and Conrad are looking into prototypes/mockups for more experience

Outstanding Action Items

• Setting up ChimeraX distribution:
  1. Conrad will implement click-through license
  2. Greg will create embedded software page with links (only)
  3. Conrad will make http reference in About panel into hyperlink
• Greg and TomG will investigate how "sym" command uses instancing