Phenix

• Fixed bug in "phenix location" (wasn't setting location)
• Further work on Randy Read's fit-in-map tool, emplace_local:
  • Interactive adjustment of search center, and size of marker indicates search size
  • Move structure to fitted position rather than open a copy
  • Use emplace_local JSON output
  • For center-of-view search center:
    • Use pivot point or fixed center of rotation (if any), otherwise...
    • Use displayed map (if only one) instead of half map
    • Improved initial Z-depth estimate (bounding box face intercepts rather then bounding-plane intercepts)
  • Elaine created documentation
  • Emplace_local now can estimate resolution, change command and tool to make resolution optional
  • Put on Toolshed
  • Awaiting emplace_local outputting transformation matrix

ChimeraX completed

• SwissDock format
• Build Structure "Invert" tab (invert chiral center) and command
• Palette and color-key support in Render By Attribute
• Structure copy/combine was using a function that modified coordinates in place rather than making a copy
  • Only mattered if transformation was non-identity, so only manifested if copied structure had been moved
• Option to deselect current selection in "Select Zone..."
• Plugged memory leak in atomic session saving (append vs. list insertion)
• Fixed Dock Prep tool to actually show follow-on dialogs
• Create CRYST1 record from mmCIF metadata