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 ​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