= 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 =
 * !DockPrep option to delete residues with incomplete backbones
 * Interpolation support for centroids in scenes
 * Switch to accessible color scheme for Sphinx documentation
 * !ViewDock
   - Report number of currently listed compounds
   - Have hotkeys honor the //sorted// column order
 * Trajectory clustering
 * Support dark mode in sequence viewer
 * Added underlying atomic support for straight helices
 * Profile Grid
   - Preference to turn off auto-association
   - Option to scroll to newly selected cells
 * "omit" keyword for trajectories
 * Added 'dockerize' build target
 * Fixed bug with mis-positioned histogram markers when placed outside data range
 * "rmsd" keyword for matchmaker command
 * Auto-break "triangle" waters
 * Made Clashes/Contacts shorter