General:
- recent commands are remembered between sessions; how many to remember is set in the Command Line preferences (formerly Midas preferences)
- can delete commands from the Command History; saving "all" is easier
- CASTp pocket measurements can be read from local files that were e-mailed to the user by the CASTp server
- new Mac Aqua-specific preferences: menus in windows (General category), window focus follows mouse (Mouse category)
New Tools:
- Color Key (Utilities) —
- creates labeled color key for figures
- can be started from Surface Color or Render by Attribute, set to the current coloring scheme
Tool Changes:
- Axes (Structure Analysis) —
- helical correction after principal component calculation now optional
- axes can be deleted or individually hidden/shown
- option to remove previous axes when creating new ones
- information can be saved to a file
- Build Structure (Structure Editing) — Modify Atom bonds/geometry specification rearranged and simplified
- Distances (Structure Analysis) — table is sortable
- MatchMaker (Structure Comparison) — RMSD header shown, other headers hidden in output sequence alignments
- Render by Attribute (Depiction, Structure Analysis) — Colors section includes button to create color key
- Sequence (Structure Analysis) — merged into Multalign Viewer, no longer implemented separately
- Surface Color (Volume Data), aka Electrostatic Surface Coloring (Surface/Binding Analysis) — Options section includes button to create color key
- Volume Series (Volume Data) — multiple series can be played simultaneously
Command Changes:
- molmap — showDialog option allows suppressing the Volume Viewer dialog
Major Bugs Fixed:
- 07/30/2008 restored better-looking default subdivision quality (affects smoothness of curved objects)
- 08/08/2008 Axes measurements based on transformed coordinates rather than untransformed (affects intermodel measurements when the models have been separately transformed)
Known Bugs:
- surfaces fail for some structures
- occasional corrupt saved images on Mac OS 10.5 / X11