General:
- Favorites menu includes "Add to Favorites/Toolbar..."
- faster protein secondary structure determination with ksdssp
New Tool:
- Surface Area/Volume (Utilities) &mdash calculate surface areas and Voronoi volumes with the StrucTools server
Tool Changes:
- Movie — support added for MMTK/NetCDF trajectory format
- Movie — RMSD maps containing all-by-all comparisons among specified frames can be calculated (for all atoms or selected atoms)
- Preferences — Reset/Restore/Save functions for all categories at once moved inside the Preferences section of Preferences Tool
- Volume Viewer — support added for APBS electrostatic potential format and TOM toolbox EM density map format
- sequence panel (opened from Model Panel) — secondary structure shown with color
New Commands:
- matrixget — write the current transformation matrices to a file
- matrixset — read and apply the transformation matrices from a file
- mmaker (matchmaker) — command implementation of MatchMaker tool; generates a sequence alignment for two structures and then superimposes the structures accordingly
- x3dsave — generate an X3D file representing the current graphical scene
Command Changes:
- hbonds has a new synonym findhbond to match the tool of the same name
- the behavior of label and rlabel has changed: label labels atoms with atom information; rlabel labels residues with residue information. (Old behavior: rlabel enabled display of residue information within an atom label, if one or more atom labels were shown for the residue; thus, label included residue information for one atom per residue depending on the state of rlabel)
Major Bugs Fixed:
- when saving JPEG images, the JPEG encoder used to fail occasionally
- ribbon style preferences could cause startup failures
- molecules with multiple surfaces are restored from session
- registering on Windows could fail due to a conflicting dll
Known Bugs:
- a deleted residue breaks user interfaces that associate structure with sequence (e.g., Multalign Viewer and sequence panel)
- the X3D representation is missing for VRML models
- the X3D representation of ribbons has all of the data, but not always in the right format
- volume rendering doesn't work correctly on Mac OS X before 10.3
- ribbon transparency doesn't work correctly
- cross-eye stereo parallax is wrong
- bond rotations in large molecules are slow