Phenix

General

• Reduce length of author list ("et al.") in citation widget
• Need to add '.bat' to Windows executables' names

Local EM Fitting

• Open sharpened maps in main thread
• Handle JSON output regardless of Phenix version
• Note the pre-fitted structures option only available in Phenix 2.0+

Fit Ligand

• Open sharpened
• Optionally show H-bonds formed by fit ligand
• Add citation info widget
• Iteration with Tom Terwilliger to get:
  • JSON output
  • Success/failure indicator
  • Reason for any failure
  • Map CC
  • Multiple fits
• Better handling of errors in threads

ChimeraX completed

• Generate mmCIF table from CRYST1 PDB metadata
• Prevent planar nitrogens from both coordinating a metal and being a donor
• Option to suppress MatchMaker parameter logging
• MUSCLE 5
• More accurate colors in Fit Cavities table
• MD plotting
• Sequence Viewer vs. Profile Grid preference (+ category menu vs. tabs)