Phenix

• Incorporated Billy's changes for finding/using Phenix on Windows
• Improved feedback when installation not found

Fit Loops

• Alert user that UNK gaps can't be modeled
• Revamped interface to focus on remodeling one section at a time
• Need to determine if phenix.fit_loops can "handle" just gaps

Emplace Local

• Randy Read paper
  • Wrote section on tool (why ChimeraX; how plugins work; plugin details)
  • Control for placing symmetry copies

ChimeraX completed

• Made tables more compact
• Don't send blank residue names to Antechamber
• idatm_failed boolean for SPICE processing
• File→Fetch by ID
• Glycosylation support in Change Chain IDs and command
• Specify model number in 'open'
• Size atoms by attribute value
• Don't output SEQRES for manually joined chains
• pbond command
• Modified sequence-header code to work in library distribution
• 'measure rotation' can now make true axis objects
• Don't send truncated HIS to Antechamber
• Modeller: handle target deletion relative to template
• Preliminary scene support
• Nuke blank chain IDs when combining models