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
    • Adjusted size of in-dialog help text
  • 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 send a problem report to Tom Terwilliger
  • Ligandfit was rejecting valid ligand PDB files

ChimeraX completed

• Nuke metadata and remap mmcif_chain_ids when combining models
• Prevent most tools from docking to the top or bottom of the main window
• "Details" column in region browser
• Added chain-attribute support to "color byattr" command and Render by Attribute tool
• Find Cavities
  • Allow customization of cavity-detection parameters
  • Cavity depth attributes/columns
  • Color cavities by depth
  • If replacing a docked dialog, dock the replacement
  • Don't recolor surface if colored externally
• Handle problem where labels get deleted before structure is opened [missing structure + morph]
• Structure matching using alignment sequences; options:

• Sequence renaming
• Aniso command
• Deployed UserError alternative for tools