So we've put a release candidate on the download page (http://www.cgl.ucsf.edu/chimera/download.html). We're hoping that if you have the time, you'll download it and bang on it and let us know about any bugs you find before it turns into a production release.
It's been a _long_ time since the previous production release (December of last year). Here are the major highlights:
General
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-> selections can be inverted (Select menu, "select" command, arrow keys)
-> additional arrow key functions:
left: undo selection
shift-left: clear selection
right: invert selection in models with selections
shift-right: invert selection in all models
-> PDB file writing can be restricted to displayed and/or selected atoms
-> Chimera scene can be exported (formats: X3D, POV-Ray, Renderman, VRML [latter surfaces only])
-> Actions...Set Pivot sets center of rotation w/o zooming
-> Help...Search Documentation searches local documentation
-> Tools menu reorganized
-> balloon help over bonds/pseudobonds includes length
-> residue labels now positioned at centroid of displayed atoms
-> new residue attribute "isHet" (whether residue is in HETATM PDB records)
-> nucleic-acid ambiguity codes can be used in subsequence searching (R=A/G, Y=C/T/U, N=A/C/G/T/U)
-> switched to Python 2.4
New Tools
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-> Attribute Calculator (Structure Analysis): generate new numerical attributes from existing ones; calculate totals or averages of an attribute
-> Color Zone (Volume Data): color surface patches near selected atoms with those atoms' colors [for GRASP surfaces and Volume Viewer/Multiscale surfaces rather than 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 (giving the illusion of the surface as a solid object rather than a hollow object)
-> Surface Color (Volume Data): color surfaces according to volume data or geometry (distance from a point, plane, or axis)
-> Electrostatic Surface Coloring (Surface/Binding Analysis): specialization of preceding tool to facilitate coloring with electrostatic volume data; also replaces DelphiViewer
-> Surface Zone (Surface/Binding Analysis): restrict GRASP or Multiscale Models surface display to zone around selected atoms
-> Values at Atom Positions (Volume Data): map volume data to atom positions; create atom attributes with the values
-> 2D Labels (Utilities): create arbitrary text labels and place them in 2D
Tool Changes
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-> Benchmark (Utilities): now also benchmarks molecule display performance
-> Demos (Demos): new Hormone-Receptor Complex demo
-> Lighting (Viewing Controls): new simplified interface available
-> MatchMaker (Structure Comparison): can include secondary-structure term in the alignment score and can iterate the fit
-> MD Movie (formerly Movie; Utilities): new "md:" prefix for metafiles; add step size option for playback; RMSD map calculation speeded up; can automatically recolor RMSD map for contrast; ability to collect atom occupancy data and display it with Volume Viewer; user-friendly interface to Movie Recorder for generating movie from trajectory
-> MultAlign Viewer (Structure Comparison): all-gap positions can be omitted from saved files; all headers available as residue attributes in associated structures; more sophisticated conservation measures available (calculated with AL2CO program); headers can be saved to a file or loaded from a file; structure association info can be saved to a file
-> Multiscale Models (Higher-Order Structure): separate surfacing threshold for CA-only chains
-> Nucleotides (Depiction): now assigns a pucker value to all sugar atoms (plane/envelope/endo/exo)
-> Per-Model Clipping (Depiction): new slab mode to show just a slice of a model
-> ViewDock (Surface/Binding Analysis): saves in sessions; H-bond statistics can included in the columns of ligand descriptors (and used for sorting)
-> Volume Viewer (Volume Data): major interface reorganization; added support for UHBD electrostatic potential (binary only), gOpenMol, and PROFEC grid formats; support added for non-orthogonal crystal data
New Commands
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-> 2dlabels: command-line version of 2D Labels tool
-> movie: command-line version of Movie Recorder tool
-> writesel: command-line version of Actions...Write List
Command Changes
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-> color: can now also color ribbons
-> British spellings added for gray, color, and center
-> match: added "iterate" keyword to allow pruning bad pairs until worst pair is below a threshold
-> matchmaker (mmaker): added keywords corresponding to new MatchMaker tool abilities
-> select: new keyword for inverting selections
-> write: keywords for restricting to displayed/selected atoms
Documentation
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-> new Attributes tutorial: covers Render by Attribute, Surface Area/Volume, Attribute Calculator, and advanced command-line usage