Phenix

General

• Reduce length of author list ("et al.") in citation widget
• Need to add '.bat' to Windows executables' names

Local EM Fitting

• Open sharpened maps in main thread
• Handle JSON output regardless of Phenix version
• Note that pre-fitted structures option only available in Phenix 2.0+

Fit Ligand

• "Show clashes" option
• Got feedback from Tom T. as to why map cropping is needed if there's a search center
• Worked on placing a ligand for specifying search center and bounds

ChimeraX completed

• Generate mmCIF table from CRYST1 PDB metadata
• Prevent planar nitrogens from both coordinating a metal and being a donor
• Option to suppress MatchMaker parameter logging
• MUSCLE 5
• More accurate colors in Fit Cavities table
• MD plotting
• Sequence Viewer vs. Profile Grid preference (+ category menu vs. tabs)