Phenix

Fit Ligand

• Emit status message when job finishes
• Optionally show H-bonds formed by fit ligand
• Add citation info widget
• Iteration with Tom Terwilliger to get:
  • JSON output
  • Success/failure indicator
  • Reason for any failure
  • Map CC
  • Multiple fits

ChimeraX completed

• Integrated LAMMPS into main ChimeraX code
• Session saving support in Profile Grids:
• Significantly improved perceived load time of large alignments
  • Suppress unnecessary copying of sequences
  • If >10000 sequences, don't use AL2CO
  • Cache sequence information when computing identity histogram
• Made "original look" preset undo tube helices
• Fixed memory leak in command atom specs
• Developer documentation:
  • Discussed the use of keyword args in commands
  • Described the Qt shim
• Structure matching using alignment sequences; options:
  • High identity
  • Iteration
  • Just active region
  • Create region showing match
• Sequence renaming
• Aniso command
• Deployed UserError alternative for tools