Phenix

• Made a release on the Toolshed

Fit Loops

• Undo (but not redo)

Local EM Fitting

• If symmetry requested but not found, log info about manually making symmetry copies
• Paper officially published, added citation widget for it

Fit Ligand

• Implemented command version
• Implemented tool UI (but only partially functional)

ChimeraX completed

• Support HTML in table cells
• Sequence viewer expand selection to columns
• If chains have been created, use that info in determining residue principal atom
• Log a message when computing secondary structure
• Label missing segments, and offer control over when they get labeled
• Stop auto-raising Log when logging occurs
• Avoid Modeller tool crash by using takeRow() instead of deleteRow()
• Have render/select histograms update if underlying values change
• Fixed bug showing alignment from MatchMaker if Smith-Waterman was used with selection restriction
• Optionally output contacts/clashes on a per-residue basis
• Also worked on: AmberTools, atom-spec parser, profile grids, match→align