= 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
      * Get toolshed/session-init funcs out of !__init!__?
  * Assign required site-visit functionality to people
  * Discussion of site visit scenarios
  * Continuation of 8-29 discussion

= Discussion =
  * Previous action items:
    * ~~Conrad '''will''' make http reference in ChimeraX About panel into hyperlink
    * ~~Greg and TomG '''will''' investigate how "sym" command uses instancing and how it is reflected in x3d output
      * x3d output now honors sym instancing and produces much smaller output
  * Chimera 1.11.2 release
    * 1.11.2 will have a working !BlastProtein
    * Need to implement fix for blastpdb before 1.11.2
      - Fix by replacing Opal script for !BlastProtein service with shell script that displays error message and exit with status 1
      - 1.11.2 will use BlastProtein2 as service name
      - Major change in nr format deflines, with different results from preformatted NCBI blast database vs one built from NCBI fasta file
      - Make sure MDA and MAV are compatible with newest blast version
    * Check for Sierra problems with touchpad and scrolling
  * 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
        * ~~Greg showed new classifier format
        * 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
      * ~~Get toolshed/session-init funcs out of !__init!__?
        * ~~Create a Bundle class and put Bundle API methods in instance with standard name in !__init!__
      * 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
        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, command line options (low priority)
        * 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
    * Matchmaker is working!
    * Interactive contact map for assemblies
    * IHM format support
      * Gaussian models
      * Issues with DOI links
    * OpenMM investigation
      * MDFF author is interested in using ChimeraX
  * 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)
    * Interface viewer (TomG)
    * 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 optical microscopy
      - Krogan?
      - ''deRisi''?
      - Chiu?
    * Allot time for Chimera 1 if site visitors are not familiar with Chimera 1
  * Continuation of 8-29 discussion

= Outstanding Action Items =
  * ~~Conrad will make http reference in ChimeraX About panel into hyperlink 
  * ~~Greg and TomG will investigate how "sym" command uses instancing
  * Conrad will make sure that template tools directory is exempt from copyright updates