= 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