Phenix

Local EM Fitting

• Results dialog improvements
  • Limits scores to a reasonable number of digits
  • Keep sharpened map if shown
  • Symmetry copies
  • In-dialog help text, and adjusted size
  • Dock dialog so it's not easily lost
• Alerted Randy that emplace_local is broken in the latest Phenix release candidate

Fit Ligand

• Sent Dorothee what I would need in ligandfit JSON output
• Tested a few systems and sent a problem report to Tom Terwilliger
  • Ligandfit was rejecting valid ligand PDB files

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