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

• 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 tool shorter