Attendees

Elaine, Eric, Greg, Conrad, TomG, TomF

Agenda

• Review action items from last meeting
• Chimera 1.11.1 release
• ChimeraX issues
  • Metadata for tools/bundles
    • Get toolshed/session-init funcs out of __init__?
• Assign required site-visit functionality to people
• Continuation of 8-29 discussion

Discussion

• Previous action items:
  • Conrad will make http reference in ChimeraX About panel into hyperlink
  • Greg and TomG will investigate how "sym" command uses instancing and how it is reflected in x3d output
• Chimera 1.11.1 release
  • Candidate releases are up except for 32-bit Windows
  • Need to implement fix for blastpdb before final 1.11.1
    • Fix by replacing Opal script for BlastProtein service with shell script that displays error message and exit with status 1
    • 1.11.1 will use BlastProtein2 as service name
    • Major change in nr format deflines
    • Wait until after general fix for blast on plato
    • Test if MDA is compatible with newest blast version
• ChimeraX issues
  • Ribbon progress
    • Lots of stuff on Elaine's documentation page
    • Conrad ported some standalone helix code into ChimeraX but needs to complete it
  • Investigate protein h-bonds/ss-bonds in mmCIF
    • Only protein h-bonds are sheet h-bonds, no helix or general h-bonds
  • Display DSSP h-bonds for comparison with other sources (e.g., FindHBond)
    • DSSP only cares about h-bonds involving backbone, no sidechain-only h-bonds
    • May be useful for 3D printing
    • Low priority for now
  • Metadata for tools/bundles
    • Change in tool/bundle template
      • Greg showed new classifier format
      • For UI purposes, there is no API for GUI options in open or save panel for bundles for now
      • For extra open/save arguments, register them in custom initialization function
    • Get toolshed/session-init funcs out of __init__?
      • Create a Bundle class and put Bundle API methods in instance with standard name in __init__
• 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 (TomG)
  • -----
  • 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

• Conrad will make http reference in ChimeraX About panel into hyperlink
• Greg and TomG will investigate how "sym" command uses instancing
• Conrad will make sure that template tools directory is exempt from copyright updates