= Phenix =

=== AlphaFold2 Barbed Wire ===
 * Show [https://pubmed.ncbi.nlm.nih.gov/40937679/ Richardson lab categorization] of !AlphaFold structures
 * Based on feedback:
   - Color atoms as well as ribbons
   - Filter out structures with missing structure from command/tool
   - Simple results dialog
   - Tweaked "uncategorized" color
 * Elaine created help pages

=== Local EM Fitting ===
 * Due to changes in Phenix's naming of default JSON output files, use explicit output file name

Put bundle with all the above on Toolshed

= ChimeraX completed =
 * Find Cavities/kvfinder improvements (Tristan suggestions)
   - Specify search box by using a set of atoms (and a pad value) instead of x/y/z/width/height/depth
   - Allow non-polymeric atoms to be treated as part of the receptor
 * Scene support
   - 2D label interpolation
   - Ribbon styles
   - Better interpolation of pseudobonds and coordinate sets
 * Made Gromacs reader use less peak memory
 * Made local Modeller execution not mistakenly require specifying a license key
 * Profile Grid
   - Show changes in prevalence based on chosen cells
   - Allow cells corresponding to a particular sequence to be chosen
   - Headers containing individual sequences
   - Turn off auto-association for very large alignments
 * Added 'is_reference' attribute to Sequence class
   - For sequences whose numbering should not be changed regardless of structure association (e.g. !UniProt)
 * OpenMM
   - Doesn't like non-unique names in a residue
   - Doesn't like missing backbone atoms
 * Now that Qt no longer remembers editor custom colors automatically, do it ourselves
 * Render By Attribute
   - Programmatically configurable
   - Show it in more cases: !Clashes/Contacts tools; defattr; measure mapvalues
 * Updated docs to use Sphinx [https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html PyData] theme
 * !ViewDock shows count of compounds listed in table