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<html><head> <link rel="icon" href="/chimera/chimera16.png" type="image/png"> <link rel="apple-touch-icon" href="images/Chimera120.png"> <link rel="stylesheet" href="/css/cgl.css" type="text/css"> <link rel="stylesheet" href="/css/chimera.css" type="text/css"> <title>UCSF Chimera Home Page</title></head><body alink="#7f1066" bgcolor="#ffffff" link="#154c5c" vlink="#7f1066">  <div style="margin-bottom: 110px;"> <img src="/images/Top.png" style="position: absolute; left: 10px; top: 10px; right: 10px;" height="86" width="95%"> <a href="/index.html"><img border="0" src="/images/DNALogo1.png" style="position:absolute; left: 10px; top: 10px;"></a> <img src="/images/TopHighlightNew.png" style="position: absolute; top: 10px; right: 10px;"> <a href="/Overview/index.html" class="top-line" style="right:325px;">about</a> <a href="/Research/index.html" class="top-line" style="right:235px;">projects</a> <a href="/Overview/staff.html" class="top-line" style="right:150px;">people</a> <a href="/Outreach/pubs/index.html" class="top-line" style="right:35px;">publications</a> <span class="second-line-shadow" style="right:254px;">resources</span> <a href="/Resources/index.html" class="second-line" style="right:255px;">resources</a> <span class="second-line-shadow" style="right:149px;">visit us</span> <a href="/Visitors/index.html" class="second-line" style="right:150px;">visit us</a> <span class="second-line-shadow" style="right:54px;">search</span> <a href="/Search/index.html" class="second-line" style="right:55px;">search</a> </div>  <div class="leftNav"> <p class="header" style="margin-top: 0px">Quick Links</p> <h4 class="menu"><a href="/chimera/docindex.html">Documentation</a></h4> <h5 class="menu"><a href="/Outreach/Tutorials/GettingStarted.html">Getting Started</a></h5> <h5 class="menu"><a href="/chimera/current/docs/UsersGuide/">User's Guide</a></h5> <h5 class="menu"><a href="/chimera/current/docs/UsersGuide/framecommand.html">Command Index</a></h5> <h5 class="menu"><a href="/chimera/tutorials.html">Tutorials</a> and <a href="/chimera/videodoc/videodoc.html">Videos</a></h5> <h5 class="menu"><a href="/chimera/data/tutorials/volumetour/volumetour.html">Guide to Volume Data</a></h5> <h5 class="menu"><a href="/chimera/docs/relnotes.html">Release Notes</a></h5> <h4 class="menu"><a href="/chimera/download.html">Download</a></h4> <h4 class="menu">Galleries</h4> <h5 class="menu"><a href="/chimera/ImageGallery/">Image Gallery</a></h5> <h5 class="menu"><a href="/chimera/animations/animations.html">Animation Gallery</a></h5> <h4 class="menu"><a href="/chimera/docs/morerefs.html">Publications</a> and <a href="/chimera/examples.html">Talks</a></h4> <h4 class="menu"><a href="/chimera/related/related.html">Related Databases and Software</a></h4> <h4 class="menu"><a href="/chimera/docs/credits.html">Citing Chimera</a></h4> <h4 class="menu"><a href="/chimera/docs/feedback.html">Contact Us</a></h4> <p class="header">Recent Citations</p> <p class="newsItem"> <a href="https://pubmed.ncbi.nlm.nih.gov/39939760" target="_blank"> Balanced plant helper NLR activation by a modified host protein complex.</a> Huang S, Wang J <i>et al.</i> <i>Nature.</i> 2025 Mar 13;639(8054):447–455. </p> <p class="newsItem"> <a href="https://pubmed.ncbi.nlm.nih.gov/39939758" target="_blank"> Activation and inhibition mechanisms of a plant helper NLR.</a> Xiao Y, Wu X <i>et al.</i> <i>Nature.</i> 2025 Mar 13;639(8054):438–446. </p> <p class="newsItem"> <a href="https://www.nature.com/articles/s41467-025-57136-7" target="_blank"> Virtual library docking for cannabinoid-1 receptor agonists with reduced side effects.</a> Tummino TA, Iliopoulos-Tsoutsouvas C <i>et al.</i> <i>Nat Commun.</i> 2025 Mar 6;16(1):2237. </p> <p class="newsItem"> <a href="https://pubmed.ncbi.nlm.nih.gov/40014714" target="_blank"> A widespread plant defense compound disarms bacterial type III injectisome assembly.</a> Miao P, Wang H <i>et al.</i> <i>Science.</i> 2025 Feb 28;387(6737):eads0377. </p> <p class="newsItem"> <a href="https://pubmed.ncbi.nlm.nih.gov/39779855" target="_blank"> RNA control of reverse transcription in a diversity-generating retroelement.</a> Handa S, Biswas T <i>et al.</i> <i>Nature.</i> 2025 Feb 27;638(8052):1122–1129. </p> <span class="more"><a href="citations.html">Previously featured citations...</a></span> </div>  <div class="news"> <p class="header" style="margin-top: 0px">Chimera Search</p> <form style="margin-bottom: 0px" action="https://www.google.com/search" name="f"> <input type="hidden" name="hl" value="en"/> <input type="hidden" name="ie" value="UTF-8"/> <input type="hidden" name="as_sitesearch" value="https://www.cgl.ucsf.edu/chimera"/> <input name="q" value=""/> <input type="submit" value="Go" name="btnSearch"/> </form> <span style="font-size:70%">Google Search</span> </p> <p class="header">News</p> <p class="newsDate">March 6, 2025</p> <p class="newsItem"> Chimera production release 1.19 is now <a href="download.html">available</a>, fixing the ability to fetch structures from the PDB (<a href="docs/relnotes/1.19.html">details...</a>). </p> <p class="newsDate">December 25, 2024</p> <p class="newsItem"> <table align="left"> <tr><td> <img src="/chimerax/images/2914530.png" style="width:25px; margin: 1px -1px; vertical-align:middle"> </tr></td> </table> The RBVI wishes you a safe and happy holiday season! See our <a href="https://www.rbvi.ucsf.edu/Outreach/card-gallery/2024-glp1/glp1.html" target="_blank">2024 card</a> and the <a href="https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html" target="_blank">gallery of previous cards</a> back to 1985. </p> <p class="newsDate">October 14, 2024</p> <p class="newsItem"> <font color="red">Planned downtime</font>: The Chimera and ChimeraX websites, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable starting Monday, Oct 14 10 AM PDT, continuing throughout the week and potentially the weekend (Oct 14-20). </p> <span class="more"><a href="news.html">Previous news...</a></span> <p class="header">Upcoming Events</p> </div> <div class="middle"> <div id="outdated-warning" style="padding: .5em; text-align: center; background-color: #FFBABA; color: #6A0E0E;"> Please note that UCSF Chimera is legacy software that is no longer being developed or supported. Users are strongly encouraged to try <a href="/chimerax/">UCSF ChimeraX</a>, which is under active development. </div> <img src="/images/titleChimera.png" height="55" width="370"> <p style="font-size: 90%; margin-bottom: 10px; margin-top: 5px;"> UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. It is available free of charge for noncommercial use. Commercial users, please see <a href="/chimera/commercial_license.html">Chimera commercial licensing</a>. </p> <p style="font-size: 90%; margin-bottom: 10px; margin-top: 5px;"> <b>We encourage Chimera users to try <a href="/chimerax/">ChimeraX</a></b> for much better performance with large structures, as well as other major <a href="/chimerax/docs/user/advantages.html" target="_blank">advantages and completely new features</a> in addition to nearly all the capabilities of Chimera (<a href="/chimerax/progress.html" target="_blank">details...</a>). </p> <p style="font-size: 90%; margin-bottom: 10px; margin-top: 5px;"> <b>Chimera is no longer under active development</b>. Chimera development was supported by a grant from the <a href="https://www.nih.gov/" target="_blank">National Institutes of Health</a> (P41-GM103311) that ended in 2018. </p>  <p class="header">Feature Highlight</p> <div class="feature" style="min-height: 200px"> <div style="min-height:220px"> <img src="/chimera/feature_highlights/emd_1116_radial.png" width="244" height="212" alt="radial surface color" HSPACE="15" TITLE="radial surface color" style="float: left;"> <a name="surfcolor_radial"> <h3 class="subHeader">Radial Coloring</h3> </a> <p> A surface can be <a href="/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html">colored radially</a>, that is, by distance from a user-specified point. Additional options include coloring by distance from an axis or a plane. Different coloring schemes can be applied. </p>  <span class="more">(<a href="/chimera/features.html">More features...</a>)</span> </div> <hr class="more"/> </div> <p/>   <p class="header">Gallery Sample</p> <div class="feature" style="min-height: 250px;" > <div style="min-height:300px"> <a href="/chimera/ImageGallery/entries/kchan/kchan.html"> <img src="/chimera/ImageGallery/entries/kchan/kchan.png" width="250px" style="margin:4px 8px" align="right" /> </a> <a href="/chimera/ImageGallery/entries/kchan/kchan.html"> <h3 class="subHeader">Sliced Potassium Channel</h3></a> <p style="margin-bottom: 0px; margin-top: 0px;"> Potassium channel (Protein Data Bank entry <a href="https://www.rcsb.org/structure/1BL8" target="_blank">1bl8</a>) on a <b>dark slate blue</b> background with potassium ions shown in <b>firebrick</b>. The channel is comprised of four chains. Each chain has been <a href="/chimera/docs/ContributedSoftware/rainbow/rainbow.html">rainbow</a>-colored from <b>blue</b> at the N-terminus to <b>red</b> at the C-terminus, but only the surface of the channel is shown. The surface has been sliced with a <a href="/chimera/docs/ContributedSoftware/per-model/per-model.html">per-model clipping</a> plane. The <a href="/chimera/docs/ContributedSoftware/surfcapper/surfcapper.html">surface cap</a> color is <b>plum</b> except with <a href="/chimera/docs/UsersGuide/colortool.html">opacity</a> set to <b>0.8</b>. The <a href="/chimera/docs/UsersGuide/sideview.html#shininess">shininess and brightness</a> have been set to <b>128</b> and <b>8</b>, respectively, and the <a href="/chimera/docs/UsersGuide/sideview.html#lighting">lights</a> on the scene have been moved from their default positions. The <a href="/chimera/docs/UsersGuide/sideview.html#effects">subdivision quality</a> (related to the smoothness of the spherical ions) is <b>5.0</b>, and the molecular surface was computed with <a href="/chimera/docs/UsersGuide/msmsattrib.html">probe radius and vertex density</a> set to <b>1.0</b> and <b>6.0</b>, respectively. <span style="font-size: 80%;">(<a href="/chimera/ImageGallery/">More samples...</a>)</span> </p> </div> </div>  </div> <p><hr align=left></p> <p align=center> <a href="/Overview/index.html">About RBVI</a> | <a href="/Research/index.html">Projects</a> | <a href="/Overview/staff.html">People</a> | <a href="/Outreach/pubs/index.html">Publications</a> | <a href="/Resources/index.html">Resources</a> | <a href="/Visitors/index.html">Visit Us</a></p> <p align=center> <font size="-2"> Copyright 2018 Regents of the University of California. All rights reserved. </font></p> </body></html>