Phenix

• Decided on implementing Randy Read's fit-in-map tool.
• Implemented command version
  • Executable name changed, so changed command name (phenix emplaceLocal) to correspond
  • Full-map arg now no longer required or accepted
    • Unclear how removing pre-fitted density will work
• Implemented most of tool GUI
  • Needs place-marker mouse-mode control

ChimeraX completed

• NIAID: Don't do missing-structure calculations when adding atoms to residue during copy
• Coordinate set playback tool speed control
• swapna command
• Ensure MatchMaker orders /A-F as expected
• NIAID: Dock Prep tool
• Sequence RMSD computation was wrong due to mis-indentation
• Compute coulombic volumes
• Developed charges for 5' phosphorylated nucleic acids
• NIAID: Have Mol2 reader add missing-structure pseudobonds and change residue names like ALAxy to just ALA
• NIAID: SDF with just a '0' in charges section means missing charges
• Sanity check PDB coordinates for NaN
• NIAID: Add Charges tool
• Support 8-character PDB IDs