= 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