For Developers:
- There have been some API changes — details can be found in the Chimera developers mailing list.
General:
- Chimera is 10-20% faster depending on what you're doing
- selections can be inverted (using the the Select menu, the command select, or arrow key shortcuts)
- new arrow key operations:
left arrow undo selection shift-left arrow clear selection right arrow invert selection (only in models containing selections) shift-right arrow invert selection (all models) - PDB file writing can be restricted to only selected and/or displayed atoms (File... Save PDB, Actions... Write PDB, "write PDB" in the Model Panel, "Write PDB" button on the Selection Inspector, the command write)
- the Chimera scene can be exported with File... Export Scene (formats: X3D, POV-Ray, RenderMan, and VRML, with the latter only including surfaces)
- in the Select menu, residue names are directly under Residue and are segregated into standard and nonstandard categories
- Select... Save Selection renamed Name Selection
- Actions and Help menus reorganized
- Actions... Set Pivot added; sets rotation center without zooming
- Help... Search Documentation added for searching local documentation
- Tools menu reorganized; new category names, removal of a few obsolete entries (MSF Viewer superseded by Multalign Viewer, AlignPlot superseded by Minrms Plot, DelPhiViewer superseded by Surface Color)
- balloon help over bonds/pseudobonds includes length
- residue labels are now positioned at the centroid of the displayed atoms, including backbone atoms when they are hidden by ribbon
- new residue attribute isHet (whether the residue is in HETATM records in the input PDB file)
- nucleic acid ambiguity codes (R = A/G, Y = C/T/U, N = A/C/G/T/U) can be used in subsequence searching (Select...Sequence... and Sequence Panel)
- N1 atom type (sp-hybridized N) split into N1+ (bonded to two other atoms) and N1 (bonded to one other atom)
- additional amino acid hydrophobicity scales (available as Define Attribute files)
- Switched to Python 2.4
New Tools:
- Attribute Calculator (Structure Analysis) — generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute
- Color Zone (Volume Data) — color surface patches near selected atoms, using the colors of those atoms (works for GRASP surfaces and surfaces from Volume Viewer and Multiscale Models, but not standard molecular surfaces)
- Demo Editor (Demos) — graphical interface for creating demos
- Movie Recorder (Utilities) — capture image frames from Chimera and assemble them into a movie file
- Surface Capping (Depiction) — cap surfaces where they intersect a clipping plane
- Surface Color (Volume Data, Surface/Binding Analysis) — color surfaces according to volume data or geometry (distance from a point, axis, or plane)
- Surface Zone (Surface/Binding Analysis) — restrict GRASP or Multiscale Models surface display to a zone around selected atoms
- Values at Atom Positions (Volume Data) — map volume data to atom positions and assign values as an attribute
- 2D Labels (Utilities) — create arbitrary text labels and place them in 2D
Tool Changes:
- Benchmark (Utilities) — molecule benchmarks added (previously only volume displays)
- Demos (Demos) — changes in demo dialog buttons/menu; demo source file format changed to XML (see new Demo Editor); older format can still be played; new Hormone-Receptor Complex Demo
- FindHBond (Structure Analysis) — see changes in "hbonds" command (below)
- Lighting (Viewing Controls) — new simplified interface with just brightness, key-to-fill ratio (contrast), and light positions
- MatchMaker (Structure Comparison) — can include a secondary structure term in the alignment score; can automatically iterate the fit
- MD Movie (formerly Movie; Utilities) — new "md:" prefix for metafiles; added step size option for replay; RMSD map calculation speeded up; can automatically recolor RMSD maps for contrast; "Analysis... Calculate occupancy" added to collect occupancy data and display it with Volume Viewer; "File... Record movie" added to facilitate image capture and assembly into a movie file
- Multalign Viewer (Structure Comparison) — Region Browser acts upon chosen region(s) (not necessarily the active region) and includes checkboxes to control which is active and which are shown in the sequence window; all-gap positions can be omitted from saved files; all headers (Consensus etc.) available as residue attributes in associated structures; more sophisticated measures of Conservation available (calculated with the program AL2CO); conservation values can be saved to a file (File... Save Conservation); associations can be saved to a file (File... Save Association Info); information to be shown as a header line (such as Conservation) can be read from an external "header definition file"
- Multiscale Models (Higher-Order Structure) — separate surfacing threshold for CA-only chains
- Nucleotides (Depiction) — now assigns a pucker value to all sugar atoms (one of plane, envelope, endo, or exo)
- Per-Model Clipping (Depiction) — new slab mode to show just a slice of a model
- ViewDock (Surface/Binding Analysis) — status saved in sessions; H-bond statistics can be included in the columns of ligand descriptors
- Volume Viewer (Volume Data) — major interface reorganization; support added for UHBD electrostatic potential (binary only), gOpenMol, and PROFEC grid formats; support added for non-orthogonal crystal data
New Commands:
- 2dlabels — create arbitrary text labels and place them in 2D; command-line implementation of 2D Labels
- movie — capture image frames and assemble them into a movie file; command-line implementation of Movie Recorder tool
- writesel — write a readable text file containing specifications of the currently selected (or unselected) items; command-line implementation of Actions... Write
Command Changes:
- color — now colors ribbons, although they can be specified independently from atoms, etc.
- British spellings added: grey can be substituted for gray, colour for color, and centre for center
- hbonds — new keywords "namingStyle" to control style of atom specification when H-bond information is written to a file, "reveal" to display residues when H-bond participants are undisplayed (corresponding options added to FindHBond)
- match — new "iterate" keyword to prune atom pairs farther than a specified distance apart from the least-squares fit
- matchmaker (mmaker) — new "iterate" keyword to prune residue pairs from the fit; new keywords to control secondary structure scoring
- select — new keywords for inverting selections
- stop — now adheres to "confirm exit" preference
- write — new keywords to restrict coordinate writing to selected and/or displayed atoms
Tutorial Changes:
- New Attributes tutorial — includes use of Render by Attribute, Surface Area/Volume, and Attribute Calculator, plus some advanced command-line usage
- other tutorials updated
Major Bugs Fixed:
- no longer hangs fetching PDB file if RCSB web site is down
- neon works on Windows
- deleting atoms that are part of a bond rotation no longer crashes chimera
- X3D output works for ribbons and VRML as well.
- a deleted residue used to break user interfaces that associate structure with sequence (e.g., Multalign Viewer and Sequence panel)
- fixed bug reading MRC files containing symmetry operators
Known Bugs:
- bond rotations in large molecules are slow
- volume rendering doesn't work correctly on Mac OS X before 10.3
- ribbon transparency doesn't work correctly on all platforms
- cross-eye stereo parallax is wrong