Phenix

• Allow development builds to be used as phenix installation
• Further work on Randy Read's fit-in-map tool, (Phenix: voyager.emplace_local, ChimeraX: Local EM Fitting):
  • Clarified wording in search-center dialog
  • Use transform from emplace_local rather than superposition
  • Make maps opaque while search sphere displayed
• Decided on fit_loops as next tool

ChimeraX completed

• Build Structure
  • Adjust Torsions (also in selection context menu)
  • Adjust Angles
• Handle Mol2 files that have GAFF types
• Charge computation falls back to more reliable method if faster method fails (courtesy Tristan)
• 'Info' commands can save to file
• Matchmaker
  • More reliably switch to 'sensible' similarity scoring matrix
  • 'reportMatrix' option
• Made hiding/closing of large numbers of models faster
  • Override Strucure 'display' attribute rather than use CLOSE_MODELS trigger
  • Batch updating of collections
• Default format/suffix handling