Attendees

Elaine, Eric, Greg, Conrad, TomG, TomF

Agenda

• Chimera 1.11.2 release
• ChimeraX issues
  • Metadata for tools/bundles
  • Segfault in threads
  • Toolshed
  • Cytoscape link
• Assign required site-visit functionality to people
• Discussion of site visit scenarios

Discussion

• Chimera 1.11.2 release
  • We have not received any reports for scrolling or gesture bugs with TomG's fixes
  • Both CATH and SCOP fetching are broken
    • CATH programmatic web access is suspended
    • SCOP still needs looking into but is close (Eric)
  • Wait for another week when notifications of new version gets delivered to users
    • TomG will send mail to chimera-users to ask people to stop avoiding Sierra
• ChimeraX issues
  • Qt UI issue
    • See if we can get floating panel not to sit in front of all other windows, even other applications (Eric)
  • MAV
    • Working on matching for site visit demos (Eric)
  • Metadata for tools/bundles
    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 (in progress, Greg) 4a. Need to add specifier for binary vs text file input
    5. Delete code for old metadata
  • Segfault in threads
    • Still affecting Scooter
    • There are three thread invocation locations involved when a crash occurs (Conrad)
  • blastpdb tool is working
  • Toolshed tool
  • Cytoscape link
• Assign required site-visit functionality to people
  • Cytoscape and REST interface (Conrad, Scooter)
    • StructureVizX and RINalyzer mostly work
  • Side view on PyQt (Greg)
  • Toolshed server side (Conrad)
    • CyAppStore running on ​https://cxtoolshed.rbvi.ucsf.edu
    • uploading works
  • Toolshed client side (Conrad)
    • toolshed tool almost works
  • Toolshed internals (Greg)
    • Need function for installing bundle from local wheel file
  • Ribbons (Conrad)
    • Half of Elaine's issues addressed
  • IHM cross-link distribution histograms (TomG)
    • Interest from SJ and Ilan
  • Interface viewer (TomG)
    • Add selection outlines on 2D plot from 3D selection (defer?)
  • IHM mmCIF support (TomG)
    • Burley and Westbrook are very impressed by image with 2DEM, crosslink, disordered region, etc.
  • MAV (Eric)
    • Opens FASTA files only (for now)
    • Shows alignments
    • Associates sequences with structures
    • Implementing site visit requirements
  • blastpdb (Conrad)
    • Works
  • 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)