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