Attendees

Elaine, Eric, Greg, Conrad, TomG, TomF, Scooter

Agenda

• Review action items from last meeting
• Chimera 1.11.1 release
• ChimeraX issues
• Meghan issues
• Assign required site-visit functionality to people
• Should GUIs, e.g., model panel,
  • log command equivalents (sometimes difficult)
  • generate command text and execute as command

Discussion

• Previous action items:
  • ChimeraX licensing
    • build_tools/copyright_update.py fixes copyrights, use "make" to run with correct arguments
    • PyQt (commercial version) is now the default window system, wx is NOT included
    • Click-through license for non-commercial ChimeraX is almost working
• Chimera 1.11.1 release
  • Start 1.11.1 candidate release on Thursday
  • Eric got his fixes in
• 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
  • Middle-mouse drag does not work right with PyQt5.7 on the Mac
    • Reported fixed in PyQt/Qt lists
      • Relevant page: ​https://codereview.qt-project.org/#/c/151407/
  • X3D export
    • Binary XML standard is out but no Python implementation
      • Ask Seva (Meghan's group) about how they use it
      • Suspend for now, pending new binary XML standard
      • Cobweb does NOT handle binary XML
    • Textures are not included
    • Want instancing to reduce output size
      • Appearance nodes use instances
      • Others need to be converted
    • ​1gcn examples
    • To be done:
      • Binary x3d
      • Triangle masks
      • -- Low priority --
      • Instancing for geometry
      • Check performance of X3D viewers before next two items
      • Single HTML file with both viewer and model information
      • Generating shims (e.g., cobweb)
      • Meshes
      • Lighting and material
      • Clip planes
      • Text
• Meghan issues
  • Harvest protein h-bonds from mmCIF/DSSP
  • Identify ss bonds
  • Struts vs h-bonds, which subset of h-bonds/ss-bonds to use
  • TomF will get presentation and discuss with Meghan
• 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)
• Should GUIs, e.g., model panel log stuff?
  • One-off action: log.
  • Discrete action in ongoing dialog: log.
  • Do it now for "obvious" panels like Save Dialog
  • Do we act-and-log or generate-command-and-execute?

Outstanding Action Items

• TomF will get answers for ChimeraX license
• Setting up ChimeraX distribution:
  1. Conrad will get copyrights into source/documentation files
  2. Greg will include PyQt in daily builds
  3. Conrad will implement click-through license
  4. Greg will create embedded software page with links (only)
  5. Greg will find a prereq package that requires a copy of the license to be included but does not install it with the software