Phenix

Fit Ligand

• Convert "ligand lengths" to angstroms
• Send cropped map
• Make command handle pre-existing model as ligand
• Interactive search adjustment:
  • center (example ligand)
  • bounds (outline box)
    • Enforce center remains within 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/copyable
• MD plotting
  • Surface areas
  • RMSDs
  • Save to CSV/TSV files
  • H-bonds
  • Save plot as image
  • Optional plotting types
  • Scalar plotting support