Phenix

Fit Ligand

• Controls for hiding density near existing structure
  • Still needs tweaking because "mark maximum" doesn't know about surface display
• Improved reliability of outline box display by using different API
• Added "conformers" command option
• Elaine added help page
• Put some less-often-used options into an "Options" area to simplify initial dialog
• Added dialog to solicit desired action if conflicting residue number provided

Phenix team will discuss what tool to work on next.

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 interpolation
  • 2D labels
  • 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
• 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
• 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