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 that pre-fitted structures option only available in Phenix 2.0+

Fit Ligand

• "Show clashes" option
• Got feedback from Tom T. as to why map cropping is needed if there's a search center
• Worked on placing a ligand for specifying search center and bounds

ChimeraX completed

• Find Cavities: show search box
• Thermal Ellipsoids
• Updating mutated sequence was slow (call for C++ residues once per character)
• Alternate parser
• Minimization command (95%)
• ViewDock
  • Made H-bonds/clashes buttons add columns
  • Refined set of options presented to user for H-bonds/clashes
  • Save Mol2 button
  • Close-compounds button
  • Preserve table state in sessions
  • Separate rating area
  • Register toolbar button itself
  • Allow user to reorder columns
  • Make description area selectable/copiable
• MD plotting
  • Surface areas
  • RMSDs
  • Save to CSV/TSV files
  • H-bonds
  • Save plot as image
  • Optional plotting types
  • Scalar plotting support