Attendees

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

Agenda

• Review action items from last meeting
• Chimera 1.11.2 release
• ChimeraX issues
  • Metadata for tools/bundles
• Assign required site-visit functionality to people
• Discussion of site visit scenarios
• Continuation of 8-29 discussion

Discussion

• Previous action items:
  • Conrad will make sure that template tools directory is exempt from copyright updates
• Chimera 1.11.2 release
  • 1.11.2 has a working BlastProtein, MAV and MDA
    • Preformatted Blast databases are being mirrored from NCBI
  • Many Sierra problems with touchpad and/or scrolling
    • Take a look at JDK fix for scrolling problem (Scooter will forward to TomG)
• 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
  • Metadata for tools/bundles
    • Change in tool/bundle template
      • 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
    • Steps in updating to new metadata
      1. Rename "tools" to "bundles", "gui.py" to "tool.py"
      2. Add support for new metadata format in toolshed
         • Including refactoring "fetch" code
         • Initialization order should be based on dependency
      3. Migrate limited set of bundles to test new code
      4. Migrate remaining bundles
      5. Delete code for old metadata
    • New toolshed core functionality
      • New deliverables: selectors, mouse modes, command line options (low priority)
      • Add --cmd option to execute ChimeraX command from command line:

        chimerax --cmd "ts load RESTServer; rest start"
        

      • Make main startup code a bundle to be called from shim code
      • Undeletable bundles
    • New toolshed UI
      • Tabbed interface for installed bundles and all bundles
      • Both will provide interface to search/browse by deliverables (tools, commands, file formats, selectors, etc)
      • Perhaps a separate "Active Tools" tool
    • Toolshed "server"
      • Have instructions from Alex Pico for installing Cytoscape AppStore
      • AppStore is running
      • Need to clear out Cytoscape data and implement wheel parsing
  • Prototype MAV displays sequence/alignment in a Qt window
  • Atom type selectors work on command line
  • IHM format support
    • Comparative models
    • Fetch from DOI links (using a hack)
    • Problem aligning comparative models with sphere models
  • OpenMM is installed
    • Tristan Croll, MDFF author, is testing out ChimeraX
• Assign required site-visit functionality to people
  • Cytoscape and REST interface (Conrad, Scooter)
  • Side view on PyQt (Greg)
  • Toolshed server side (Conrad)
  • Toolshed client side (Greg)
  • Ribbons (Conrad)
  • IHM cross-link distribution histograms (TomG)
  • Interface viewer (TomG)
    • Add selection outlines on 2D plot from 3D selection
  • IHM mmCIF support (TomG)
  • MAV (Eric)
  • blastpdb (Conrad)
  • Reach goals
    • String database (Scooter, Conrad)
    • Hydrogen bonds and contacts (Eric)
    • Link to NGL, LiteMol (Scooter, Conrad, Greg)
    • Molprobity on Opal (Scooter)
    • Domains
      • Web service, Uniprot? (Eric)
      • Integration into hierarchy (Eric)
      • Interactive 2D graph (team)
    • Hierarchy browser
    • UI cleanup (team)
• Site visit
  • Plan on three or four shorter DBP-based "vignettes" instead of two longer scenarios
  • Vignette with presenters:
    • Sali and IHM
    • van den Bedem and contact networks
    • Horwitz and Johnson and optical microscopy
    • Krogan?
    • deRisi student?
    • Chiu?
    • Developer testimonial from Tristan
  • Allot time for Chimera 1 if site visitors are not familiar with Chimera 1
    • Waiting for committee member list
  • Need agenda
    • Vignette titles and number of vignettes
    • Approximate times
    • Order of presentation
• Continuation of 8-29 discussion

Outstanding Action Items

• None