Attendees

• Eric, Greg, TomF, Conrad, Scooter, Elaine

Agenda

• Action items
• ChimeraX
  • PyQt license needs to be renewed soon
  • Toolbar and button bar unification
  • Write mmCIF files while keeping unused tables
  • Manager/provider toolshed functionality (#1661)
  • RBVI bundles on toolshed
    • Change build process to trim down list of bundles in standard release while still testing toolshed-only bundles
  • Stable APIs, #922
  • Documentation strategy
  • 1.0 features (roadmap)
• Possibilities for Eric's SOW

Discussion

• ChimeraX
  • PyQt license needs to be renewed soon
    • Our license expires on April 27th
    • We currently have a 3-user license and the renewal fee is $960.
    • Verify that 5.12.1 fixes browser history bug
    • Greg will build and test latest release for known problems
    • If there are no problems, then consider moving to PySide2
    • PySide2 (which requires 5.12) may be an adequate replacement for PyQt
  • Toolbar and button bar unification
    • Add comments to toolbar-unification
    • Greg will implement ribbon in Qt
    • New ribbon UI code will allow tools to use ribbon widget
      • Call it tabbed toolbar instead of "ribbon"
  • Write complete mmCIF files
    • Tables that we read but do not change
      • Done
    • Tables that we read and change
      • BUG: Need to keep additional information like sheet, helix registration, h-bond class, etc for tables that we read
      • BUG: Need to generate sheet information when ksdssp is run
      • Atomic coordinates and sequence information
        • Must write new version
      • Secondary structure, h-bonds
      • What tables does RCSB/PDB deposition require? Do we need to preserve information from input file if they get overridden by the deposition process?
        • Elaine: deposition requires author info, polymer sequences and source organisms, correct HETRES names, atomic coordinate file, and various other experimental data depending on the method of structure determination (e.g. structure factors from X-ray) and computational processing (e.g. constraints). See ​https://www.wwpdb.org/deposition/deposition-resources
    • Tables that we do not read
      • Squirrel away or reread on write
      • How big are the unused tables?
  • Manager/provider toolshed functionality (#1661)
    • Conrad will work on this
  • Putting RBVI bundles on toolshed
    • Want separate run-time vs build-time dependencies in bundle_info.xml
    • Visit the bundle-release page (from intranet) and release your bundles
    • Need to segregate "standard" bundles from "extra" bundles
  • What happens when restoring a session that uses an uninstalled tool?
    • There is a manifest of bundles referenced by session file
    • Need to detect missing bundles
      • Show warning or offer to install bundle?
      • Restore rest of session or give up or ask user?
      • What about gui vs nogui?
        • Currently, tools are skipped in nogui mode
        • Might get unnecessary warning about missing bundle that won't be used for restoring session in nogui mode
  • Stable APIs
    • See action items
  • Move to github
    • Move to private RBVI github project
      • Easier to share with collaborators with github admin tools
      • "pull requests" should simplify enhancement/fix submission
      • will not happen that soon

Action Items

• Greg will test latest PyQt/Qt release
• Greg will find out the fraction of mmCIF files that are not used by ChimeraX (by percentage and by absolute size)
• Conrad will create ticket for extending mmCIF writing to include missing tables
• Conrad will create tickets for BUGS listed above (if they don't already exist)
  • for the first one, see ChimeraX #1021 and possibly #1489 (and Chimera tickets 325 and possibly 10113 and 12200 are all along these same lines, of which 325 is a more specific description of secondary structure information loss)
  • Elaine: wwPDB deposition instructions say nothing about secondary structure. Conclusion: it must be generated after deposition by the wwPDB semiautomated annotation pipeline, so these info-loss bugs are mainly trouble for users who write PDB/mmCIF for reasons other than deposition.