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 ----------- -> 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 --------------- -> 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 -------------------- -> 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 ------------------------ -> 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 ----------------------------- -> 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 ---------------------- -> new Attributes tutorial: covers Render by Attribute, Surface Area/ Volume, Attribute Calculator, and advanced command-line usage full release notes are at: http://www.cgl.ucsf.edu/chimera/docs/ relnotes/1.2172.html Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu