<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hello everybody,</div><div>A new production release of UCSF Chimera (version 1.6) is 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>This will be the last Chimera release supporting Mac PowerPC platforms</div><div>and OS X 10.5 (Leopard).</div><div><br></div><div>New features include a Rapid Access interface to frequently used data </div><div>and tools, new ribbon spline options, improved transparency rendering, </div><div>new fetch type: Uniprot protein sequence and annotations, and several </div><div>options for fitting atomic structures into density maps: global search, </div><div>iterative sequential fitting, symmetric fitting, etc.</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/1.6.html">http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.6.html</a>></div><div><br></div><div>Graphics, Depiction: </div><div>* new spline options for ribbon closer to backbone atom positions</div><div>* new initial model colors, pastel rather than saturated</div><div>* improved transparency rendering (global single-layer on by default)</div><div>* 3D labels drawn on top by default</div><div>* fancy backgrounds: images from files, color gradients from Palette Editor</div><div>* options for cleaner pocket/tunnel surface display (see "sop" command)</div><div><br></div><div>Structure Analysis and Modeling:</div><div>* AddH allows specifying less common states of Asp, Glu, Lys, Cys</div><div>* FindHBond can label H-bonds with distances</div><div>* Blast Protein shows more info for PDB hits (ligands, resolution, etc.)</div><div>* Build Structure improvements for joining peptides, swapping substituents</div><div>* tools to change chain IDs, renumber residues</div><div>* minimization:</div><div> - can be conjugate gradient (previously steepest descent only)</div><div> - parts of structures can be ignored</div><div>* distance and angle plotting for trajectories</div><div>* Cage Builder tool for generating polyhedral cage models</div><div><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebuilder.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebuilder.html</a>></div><div>* interface to MultiFit web service (simultaneous rigid fitting of </div><div> multiple structures to density, developed by the Sali Lab, UCSF)</div><div>* "fitmap" command:</div><div> - global search with random initial placement </div><div> - iterative sequential fitting</div><div> - symmetric fitting</div><div>* "measure" command options:</div><div> - map symmetry</div><div> - surface contact area</div><div> - center of mass</div><div><br></div><div>User Interface and I/O: </div><div>* Rapid Access interface to frequently used data and tools shown at startup,</div><div> can be hidden/shown at any time by clicking the lightning-bolt icon</div><div><<a href="http://www.cgl.ucsf.edu/chimera/1.6/docs/UsersGuide/rapid.html">http://www.cgl.ucsf.edu/chimera/1.6/docs/UsersGuide/rapid.html</a>></div><div>* caching fetched data is turned on by default </div><div>* scaling with mouse/touchpad scrolling can be turned off (Mouse prefs)</div><div>* Model Panel:</div><div> - group/ungroup function, such as for NMR ensembles</div><div> - functions reorganized into favorites/all</div><div>* new input types: SPHGEN spheres, Maestro/Glide docking output (ViewDock)</div><div>* WebGL export (experimental feature)</div><div><br></div><div>Sequence-related:</div><div>* new fetch type UniProt: protein sequence and feature annotations</div><div>* Multalign Viewer:</div><div> - UniProt features can be mapped onto already open sequences</div><div> - Region Browser improvements for handling feature annotation regions</div><div> - calculation of region overall RMSD</div><div> - interface to Modeller homology modeling allows including water, other HET</div><div><br></div><div>Enjoy! On behalf of the Chimera team,</div><div><br></div><div><div>--Eric</div><br><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu/">http://www.cgl.ucsf.edu</a></font></div><div><br></div></div></span></div></div></body></html>