Phenix

Fit Loops Improvements

• Use JSON output
• Reworked command to use atom spec instead of chain ID and start/end residue numbers
  • Warn if spec selects nothing
• Reported (additional) fit-loops bugs:
  • JSON option not working
  • JSON output includes null results
  • Chain ID w/o start/end res numbers does whole structure
  • Python IndexError into solution list
  • Phenix's Python 3.10 build basically doesn't work
    • Same problem as ChimeraX had: automatic type conversion to C/C++ disabled
• Preliminary results-viewer tool

ChimeraX completed

• Updated programming tutorial to mention UI convenience classes
  • Data lists/menus (*e.g.* StructureList)
  • Remember-able options (*e.g.* FontOption)
  • Python-data tables
• Allow specifying chain association along with UniProt fetch
• Can now invert selection just in models with selections (+ arrow key support)
• IUPAC fetch
• Context-menu entry to focus on residue in sequence viewer
• Use HyperKitty search of mailing-list archives instead of Google search
• Make name column in Model Panel wider when names are long, and show tooltip for long names
• Use C4' for sequence RMSD when appropriate
• Allow setting all alt locs at once in Altloc Explorer
• Suppressed asking for format when open .cif files
• Improve variability of model colors past builtin set
• Added looping control to playback slider