Attendees

Elaine, Eric, Greg, TomF, TomG, Conrad, Scooter

Agenda

• Review action items from last meeting
• Symmetry web service - need documented API
• Discuss 1.11 release
• ChimeraX home page
• Chimera stereo announcement (​UCSF Chimera Documentation Index)
• Change session restore API so objects constructed in normal Python fashion rather than separating new and init. Needed to make it easy for outside developers (TomG)
• mmCIF support effort, Phenix and COOT

Discussion

• Chimera 1.11
  • Need to test Tk 8.6.5- builds on all platforms
• Symmetry web service - need documented API
  • Waiting on Andreas for documentation
• Chimera home page is complete for now
  • URL in installer works
  • Need to make symlink in public tree to docs so that "preview" URLs do not appear in public pages (Scooter, Elaine)
  • Make sure preview.rbvi.ucsf.edu/chimerax works
• Send out Chimera stereo announcement to chimera-users (Elaine)
• Need proposal for new restore API (ChimeraX team, TomG lead) to simplify writing session restore code for developers
• mmCIF files from Oliver did not work
  • Phenix mmCIF is missing entity_polyseq table that specifies SEQRES-equivalent information. Need to guess at what residues are connected and where chain breaks appear.
  • COOT dumps a PDB file into an mmCIF atom_site table. No entity_polyseq table. All atoms in same entity with duplicate values in several fields. Works fine in COOT, Phenix and PyMol according to Oliver.
  • PDB asks for large files in mmCIF file using Phenix or CCP4. mmCIF from Phenix is first generated and then post-processed into acceptable submission form. Get Oliver to run the Phenix standalone program? (TomG) Also ask about CCP4 and RefMac mmCIF output.

Outstanding Action Items

• Friends and Family bugs outstanding
  • Ribbon flips too often (Conrad)
    • Will try out "no orientation atom" method
  • Stretch goals
    • Side view elements displays but need to make interactive (Greg)
    • Finish mmCIF NMR structure support, need to copy secondary structure data to all models (Greg)
    • Figure out and fix Mac OS X runtime linking bug (TomG/Greg/Conrad)
    • Check executables and dynamic libraries to make sure they only reference internal or standard libraries (Greg)
• Chimera 1.11 release:
  • Build with Tk 8.6.5- in daily build (​ticket 14424)
    • Mac - balloons not working quite right
    • Windows - needs to build
    • Linux - need to be tested