Phenix

Fit Loops

• Revamped command/backend to handle possibly remodeling *only* a gap (no side residues)
• Fixed ChimeraX bug that incorrectly sequenced newly modeled gap residues
• Have tool warn user when modeling too many residues

Emplace Local

• Tool interface tweaks based on feedback
  • Left-align text
  • Align check boxes
  • Space between check boxes and bottom buttons

ChimeraX completed

• Repeat last phi/psi in build structure if needed
• Sequential model display controls in model panel
• 'altlocs show/hide' command
• Log now notes that an opened structure has altlocs
• 'combine' command can retain chain IDs; smartened up combining sequences of combined chains
• Swapaa/na allows multiple types
• Work on moving to AmberTools23
• Investigate garbage-collection crashes
• Tweaks to atom typing for SPICE
• Join models through non-peptide bond