= 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 [http://www.cgl.ucsf.edu/home/meng/chimera2/user/commands/cartoon3.html 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