<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hello everybody,</div><div>The official 1.7 production release of UCSF Chimera is now available:</div><div><a href="http://www.cgl.ucsf.edu/chimera/download.html">http://www.cgl.ucsf.edu/chimera/download.html</a></div><div><br></div><div>Download is free for noncommercial use.</div><div>Platforms: Windows, Mac, Linux, including 64-bit versions (recommended</div><div>for working with large datasets on machines with at least 4GB memory).</div><div>Note: 1.6 was the last version to support Mac PPC and OS X 10.5.</div><div><br></div><div>New features include faster loading and graphics, improvements in</div><div>lighting and interactive shadows, "click-to-center" mouse mode,</div><div>map display as orthogonal planes, interface to Modeller for building</div><div>missing loops, Animation timeline, enhanced commands for animation,</div><div>interfaces to PDB2PQR, APBS, and AutoDock Vina single-ligand docking.</div><div><br></div><div>More details are given below; see release notes for the full list:</div><div><a href="http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.7.html">http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.7.html</a></div><div><br></div><div>Graphics, Depiction: </div><div>* faster loading of large molecules</div><div>* faster graphics on many systems; target frame rate raised to 60 fps</div><div>* interactive shadows: finer quality; available on more systems</div><div>* glossy default lighting, better control over contrast</div><div>* users can create custom presets</div><div>* 2D Labels can have backgrounds (colored rectangles beneath)</div><div>* PipesAndPlanks can color SSEs uniquely, show arrowheads</div><div>* Actions...Color menu works on axis, plane, and centroid objects</div><div>* CASTp pocket display omits small surface fragments</div><div>* "surface" and "sop" command options to hide small fragments</div><div><br></div><div>Animation:</div><div>* Animation tool allows placing scenes and simple actions </div><div> (rock, roll) along a timeline to define a movie</div><div>* new output movie formats H.264, VP8/WebM, Theora</div><div>* "play" command to animate complex motions like radial explosion</div><div>* "transparency" command to set transparency of atoms, ribbons, etc.</div><div> without otherwise changing their colors, can be applied gradually</div><div>* "movie" command usability improvements </div><div>* "perframe" allows embedding other commands directly, substituting</div><div> variables other than frame count, executing at multiframe intervals</div><div>* "roll" and "turn" command options for precession motion</div><div><br></div><div>Structure Analysis and Modeling:</div><div>* AmberTools updated to v12, default charges etc. now Amber ff12SB</div><div>* "click-to-center" mouse mode (default Ctrl-right button)</div><div>* "show distances to nearby residues" added to atom context menu</div><div>* interface to Modeller for building missing segments </div><div>* interface to APBS Poisson-Boltzmann electrostatics calculations</div><div>* interface to PDB2PQR charge and radius assignment</div><div>* interface to AutoDock Vina single-ligand docking</div><div>* ViewDock support for AutoDock/Vina .pdbqt, GOLD .mol2 files</div><div>* MD Movie can calculate average structures, plot RMSD vs. frame,</div><div> read GROMACS .xtc format; occupancy calculation can treat atoms </div><div> as VDW spheres (as opposed to points only)</div><div>* Build Structure bond length slider, bond angle control</div><div>* Multalign Viewer can use a subset of the existing sequences</div><div> (rather than all) to guide alignment of a new sequence; the</div><div> Region Browser lists individual-sequence regions separately </div><div> (now that a sequence can have many UniProt annotations)</div><div><br></div><div>Density Maps:</div><div>* Volume Viewer orthogonal planes feature</div><div>* Volume Tracer default mode includes placing markers on planes</div><div>* "fitmap" option to fit multiple models independently</div><div>* "vop cover" can extend a map using its symmetries </div><div><br></div><div>Enjoy! On behalf of the Chimera team,</div><div><br></div><div>--Eric</div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><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 class="Apple-converted-space"> </span></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 class="Apple-converted-space"> </span></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="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span>
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