Phenix

AlphaFold2 Barbed Wire

• Show ​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

• Have ViewDock hotkeys honor the *sorted* column order
• Trajectory clustering
• Support dark mode in sequence viewer
• Added underlying atomic support for straight helices
• Option to scroll to newly selected cells in Profile Grid
• "omit" keyword for trajectories
• Added 'dockerize' build target
• Fixed bug with mis-positioned histogram markers when placed outside data range
• Now that Qt no longer remembers editor custom colors automatically, do it ourselves
• "rmsd" keyword for matchmaker command
• Auto-break "triangle" waters
• Made Clashes/Contacts shorter