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

• 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 ​PyData theme
• ViewDock shows count of compounds listed in table