Phenix

Fit Ligand

• Controls for hiding density near existing structure
  • Still needs tweaking because "mark maximum" doesn't know about surface display
• Improved reliability of outline box display by using different API
• Added "conformers" command option
• Elaine added help page
• Put some less-often-used options into an "Options" area to simplify initial dialog
• Added dialog to solicit desired action if conflicting residue number provided

Phenix team will discuss what tool to work on next.

ChimeraX completed

• ViewDock
  • Don't forget about hidden ligands when saving session
• Fixed bug where deleting atoms of a model and its submodels would cause a crash
• Moved Log settings from main ChimeraX preferences to the Log tool
• Speeded up opening large ligand files by 2x
  • Bottleneck was chain-reporting code for NMR ensembles
• Altloc Explorer
  • Button to show/hide all existing altlocs
  • Report occupancy in tooltip (also in main 3D window)
• ProfileGrid
  • Reporting column info on the fly too slow for very large alignment; for those only report on hover
• Added ability to time out / continue long-running blocking jobs
• Alert users to use ASCII paths for Gromacs trajectories
• Scenes
  • Skip models that don't save in sessions (e.g. individual 2D labels)
  • Interpolation of coordinate sets
  • Catch error restoring scene with deleted structure elements, warn user, and restore what we can
  • Remember more structure attributes in scenes, and interpolate simple numeric ones
  • Tool:
    • Save→Add and separate Add/Update buttons
    • Drag and drop to reorder scenes
    • When adding scene, ignore conflicting name if it was automatically generated