Attendees

Elaine, Eric, Greg, Conrad, TomG, TomF

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:
  • None
• Chimera 1.11.2 release
  • Eric got new rotamer library, defer to later release
  • Many Sierra problems with touchpad and/or scrolling
    • Take a look at JDK fix for scrolling problem (Scooter will forward to TomG)
    • Conrad will bring laptop in on Monday to show IDLE crash in same place
    • Defer release in hopes of fixing this bug first
    • TomG will ask Briana(?) to test 1.10 for crashes
• ChimeraX issues
  • Ribbon progress
    • Lots of stuff on Elaine's ​documentation page
    • Conrad will check out nucleosome ribbon display
  • 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
         • Include backwards compatibility with bundles with old metadata style code
         • 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"
      • Need to implement wheel upload to update app store database and display
        • Define where resources are found in wheels, e.g., metadata, icon, screenshot, etc.
  • Prototype MAV displays sequence/alignment in a Qt window
    • Structure-sequence association works but no user visible effects
  • IHM format support
    • TomG met with SJ and Ilan about nup82 (not promising)
      • Data is all in SJ's personal Dropbox folder and need to be uploaded to (private) github
      • SJ has no time to work on it this week
      • A lot of data is missing (sequence alignment, localization densities, unaligned ensembles) or poorly formatted (e.g., ENDMOL instead of ENDMDL)
  • OpenMM is installed
    • Tristan Croll, MDFF author, is testing out ChimeraX
    • Croll is working with Peter Eastman on OpenMM bug
    • Also testing out Chai3D haptics toolkit and Falcon device
    • Croll mentioned that people were impressed by ChimeraX at CCPEM
• Assign required site-visit functionality to people
  • Cytoscape and REST interface (Conrad, Scooter)
    • rest_server bundle is committed
    • list_info bundle is under way
    • need simplified "findclash" command
  • Side view on PyQt (Greg)
  • Toolshed server side (Conrad)
    • CyAppStore running on ​https://cxtoolshed.rbvi.ucsf.edu
    • need wheel uploading
  • Toolshed client side (Greg)
  • Ribbons (Conrad)
  • IHM cross-link distribution histograms (TomG)
    • Interest from SJ and Ilan
  • 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
• Continuation of 8-29 discussion

Outstanding Action Items

• None