<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">So we've put a release candidate on the download page (<A href="http://www.cgl.ucsf.edu/chimera/download.html">http://www.cgl.ucsf.edu/chimera/download.html</A>). 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.<DIV><BR class="khtml-block-placeholder"></DIV><DIV>It's been a _long_ time since the previous production release (December of last year). Here are the major highlights:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>General</DIV><DIV>-----------</DIV><DIV>-> selections can be inverted (Select menu, "select" command, arrow keys)</DIV><DIV>-> additional arrow key functions:</DIV><DIV> left: undo selection</DIV><DIV> shift-left: clear selection</DIV><DIV> right: invert selection in models with selections</DIV><DIV> shift-right: invert selection in all models</DIV><DIV>-> PDB file writing can be restricted to displayed and/or selected atoms</DIV><DIV>-> Chimera scene can be exported (formats: X3D, POV-Ray, Renderman, VRML [latter surfaces only])</DIV><DIV>-> Actions...Set Pivot sets center of rotation w/o zooming</DIV><DIV>-> Help...Search Documentation searches local documentation</DIV><DIV>-> Tools menu reorganized</DIV><DIV>-> balloon help over bonds/pseudobonds includes length</DIV><DIV>-> residue labels now positioned at centroid of displayed atoms</DIV><DIV>-> new residue attribute "isHet" (whether residue is in HETATM PDB records)</DIV><DIV>-> nucleic-acid ambiguity codes can be used in subsequence searching (R=A/G, Y=C/T/U, N=A/C/G/T/U)</DIV><DIV>-> switched to Python 2.4</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>New Tools</DIV><DIV>---------------</DIV><DIV>-> Attribute Calculator (Structure Analysis): generate new numerical attributes from existing ones; calculate totals or averages of an attribute</DIV><DIV>-> 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]</DIV><DIV>-> Demo Editor (Demos): graphical interface for creating demos</DIV><DIV>-> Movie Recorder (Utilities): capture image frames from Chimera and assemble them into a movie file</DIV><DIV>-> 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)</DIV><DIV>-> Surface Color (Volume Data): color surfaces according to volume data or geometry (distance from a point, plane, or axis)</DIV><DIV>-> Electrostatic Surface Coloring (Surface/Binding Analysis): specialization of preceding tool to facilitate coloring with electrostatic volume data; also replaces DelphiViewer</DIV><DIV>-> Surface Zone (Surface/Binding Analysis): restrict GRASP or Multiscale Models surface display to zone around selected atoms</DIV><DIV>-> Values at Atom Positions (Volume Data): map volume data to atom positions; create atom attributes with the values</DIV><DIV>-> 2D Labels (Utilities): create arbitrary text labels and place them in 2D</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Tool Changes</DIV><DIV>--------------------</DIV><DIV>-> Benchmark (Utilities): now also benchmarks molecule display performance</DIV><DIV>-> Demos (Demos): new Hormone-Receptor Complex demo</DIV><DIV>-> Lighting (Viewing Controls): new simplified interface available</DIV><DIV>-> MatchMaker (Structure Comparison): can include secondary-structure term in the alignment score and can iterate the fit</DIV><DIV>-> 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</DIV><DIV>-> 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</DIV><DIV>-> Multiscale Models (Higher-Order Structure): separate surfacing threshold for CA-only chains</DIV><DIV>-> Nucleotides (Depiction): now assigns a pucker value to all sugar atoms (plane/envelope/endo/exo)</DIV><DIV>-> Per-Model Clipping (Depiction): new slab mode to show just a slice of a model</DIV><DIV>-> ViewDock (Surface/Binding Analysis): saves in sessions; H-bond statistics can included in the columns of ligand descriptors (and used for sorting)</DIV><DIV>-> 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</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>New Commands</DIV><DIV>------------------------</DIV><DIV>-> 2dlabels: command-line version of 2D Labels tool</DIV><DIV>-> movie: command-line version of Movie Recorder tool</DIV><DIV>-> writesel: command-line version of Actions...Write List</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Command Changes</DIV><DIV>-----------------------------</DIV><DIV>-> color: can now also color ribbons</DIV><DIV>-> British spellings added for gray, color, and center</DIV><DIV>-> match: added "iterate" keyword to allow pruning bad pairs until worst pair is below a threshold</DIV><DIV>-> matchmaker (mmaker): added keywords corresponding to new MatchMaker tool abilities</DIV><DIV>-> select: new keyword for inverting selections</DIV><DIV>-> write: keywords for restricting to displayed/selected atoms</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Documentation</DIV><DIV>----------------------</DIV><DIV>-> new Attributes tutorial: covers Render by Attribute, Surface Area/Volume, Attribute Calculator, and advanced command-line usage</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>full release notes are at: <A href="http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2172.html">http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2172.html</A></DIV><BR><BR><DIV> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Eric Pettersen</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>UCSF Computer Graphics Lab</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></FONT></P> <BR class="Apple-interchange-newline"> </DIV><BR></BODY></HTML>