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<html><head> <link rel="icon" href="/chimera/chimera16.png" type="image/png"> <link rel="stylesheet" href="/css/cgl.css" type="text/css"> <link rel="stylesheet" href="/css/chimera.css" type="text/css"> <title>UCSF ChimeraX 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="/chimerax/index.html">UCSF ChimeraX Home</a></h4> <h4 class="menu"><a href="/chimerax/docs/user/advantages.html">Advantages</a></h4> <h4 class="menu"><a href="/chimerax/docs/index.html">Documentation</a></h4> <h5 class="menu"><a href="/chimerax/docs/user/index.html">User Guide</a></h5> <h5 class="menu"><a href="/chimerax/tutorials.html">Tutorials</a> and <a href="/chimerax/docs/videos">Videos</a></h5> <h5 class="menu"><a href="/chimerax/docs/presentations.html">Presentations</a></h5> <h4 class="menu"><a href="/chimerax/download.html">Download</a></h4> <h5 class="menu"><a href="https://cxtoolshed.rbvi.ucsf.edu/">Toolshed</a></h5> <h5 class="menu"><a href="/chimerax/stats.html">Statistics</a></h5> <h4 class="menu"><a href="/chimerax/docs/credits.html">Citing ChimeraX</a></h4> <h4 class="menu"><a href="/chimerax/docs/contact.html">Contact Us</a></h4> <h4 class="menu"><a href="/chimerax/related/index.html">Related Software</a></h4> <p class="header">Featured Citations</p> <p class="newsItem"> <a href="https://pubmed.ncbi.nlm.nih.gov/40146832" target="_blank"> Running a genetic stop sign accelerates oxygen metabolism and energy production in horses.</a> Castiglione GM, Chen X <i>et al.</i> <i>Science.</i> 2025 Mar 28;387(6741):eadr8589. </p> <p class="newsItem"> <a href="https://www.nature.com/articles/s41586-024-08493-8" target="_blank"> Structure and mechanism of the Zorya anti-phage defence system.</a> Hu H, Popp PF <i>et al.</i> <i>Nature.</i> 2025 Mar 27;639(8056):1093-1101. </p> <p class="newsItem"> <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11936420/" target="_blank"> Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland.</a> Almeida GMF, Arriaga I <i>et al.</i> <i>eLife.</i> 2025 Mar 25;13:RP103492. </p> <p class="newsItem"> <a href="https://pubmed.ncbi.nlm.nih.gov/40112058" target="_blank"> In-cell architecture of the mitochondrial respiratory chain.</a> Waltz F, Righetto RD <i>et al.</i> <i>Science.</i> 2025 Mar 21;387(6740):1296-1301. </p> <p class="newsItem"> <a href="https://pubmed.ncbi.nlm.nih.gov/39880952" target="_blank"> Structure and mechanism of vitamin-K-dependent γ-glutamyl carboxylase.</a> Wang R, Chen B <i>et al.</i> <i>Nature.</i> 2025 Mar 20;639(8055):808–815. </p> <span class="more"><a href="citations.html">More citations...</a></span> </div>  <div class="news"> <p class="header" style="margin-top: 0px">News</p> <p class="newsDate">March 19, 2025</p> <p class="newsItem"> <table align="left"> <tr><td> <img src="/chimerax/images/wiley-smallest.png" alt="Wiley most-cited-paper medallion" style="width:60px; margin: 1px -1px; vertical-align:middle"> </tr></td> </table> <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/pro.4792" target="_blank">UCSF ChimeraX: Tools for structure building and analysis</a> is one of the 10 most cited papers published in <i>Protein Science</i> in 2023! </p> <p class="newsDate">March 1, 2025</p> <p class="newsItem"> <image width="12px" src="/chimerax/images/bluesky.png" alt="Bluesky logo"> Follow UCSF ChimeraX on BlueSky! <a href="https://web-cdn.bsky.app/profile/chimerax.ucsf.edu" target="_blank">@chimerax.ucsf.edu</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> <span class="more"><a href="news.html">Previous news...</a></span> <p class="header">Upcoming Events</p> </div>  <div class="middle"> <br> <h2>UCSF ChimeraX</h2> <p style="font-size: 90%; margin-bottom: 10px; margin-top: 5px;"> UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the <a href="https://www.rbvi.ucsf.edu/">Resource for Biocomputing, Visualization, and Informatics</a> (RBVI), following <a href="https://www.rbvi.ucsf.edu/chimera/">UCSF Chimera</a>. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use. Commercial users, please see <a href="/chimerax/commercial_license.html">ChimeraX commercial licensing</a>. </p> <p style="font-size: 90%; margin-bottom: 10px; margin-top: 5px;"> ChimeraX is developed with support from <a href="https://www.nih.gov/" target="_blank">National Institutes of Health</a> R01-GM129325. </p> <p style="font-size: 90%; margin-bottom: 10px; margin-top: 5px;"> <image width="12px" src="/chimerax/images/bluesky.png" alt="Bluesky logo"> ChimeraX on Bluesky: <a href="https://web-cdn.bsky.app/profile/chimerax.ucsf.edu" target="_blank">@chimerax.ucsf.edu</a>  <p class="header">Feature Highlight</p> <div class="feature" style="min-height: 200px">  <div style="min-height:320px"> <a href="feature_highlights/model-pdl.png"> <img src="feature_highlights/model-pdl.png" width="425px" height="317px" alt="heterodimer modeling screenshot" hspace="15px" title="click to enlarge..." style="float:left; margin:2px 12px 2px 1px; border:1px solid black"></a> <a name="multichain-modeller"></a> <h3 class="subHeader">Multichain Comparative Modeling</h3> <p> <a href="/chimerax/docs/user/tools/modeller.html"><b>Modeller Comparative</b></a> is an interface to <a href="https://www.salilab.org/modeller/" target="_blank">Modeller</a> for comparative (“homology”) modeling of proteins and protein complexes. </p><p> The example shows modeling the human (shades of blue) from the mouse (brown and tan) complex of programmed death-1 (PD-1) with its ligand PD-L2, PDB <a href="https://www.rcsb.org/structure/3BP5" target="_blank">3bp5</a>. </p><p> Comparative modeling requires a template structure and a target-template sequence alignment for each unique chain. The sequences of human PD-1 and PD-L2 targets were fetched from <a href="https://www.uniprot.org/" target="_blank">UniProt</a> and associated with the corresponding chains in the template structure, see <a href="feature_highlights/model-pdl-setup.cxc">model-pdl-setup.cxc</a>. (Pairwise or multiple sequence alignments could have been used, but in this case, the template structure was simply associated with the target sequence.) Sequence-structure association shows mismatches in the <a href="/chimerax/docs/user/tools/sequenceviewer.html"><b>Sequence Viewer</b></a>: pink boxes for sequence differences between mouse and human, and gray outlines around the parts missing from the structure. </p><p> Three models were made with with default settings (other than the number of models), and the best-scoring model is shown. Two positions where sequence differences change the interfacial H-bonds are displayed. </p>  <span class="more"><a href="/chimerax/features.html">More features...</a></span > </div> <hr class="more"/> </div>  <p/>  <p class="header">Example Image</p> <div class="feature" style="min-height: 250px;" >  <div style="min-height:250px"> <a href="gallery_samples/bfactor.png"> <img src="gallery_samples/bfactor.png" width="350px" height="250px" alt="HIV-1 protease B-factor coloring" hspace="15px" title="click to enlarge..." style="float: left;"></a> <a name="bfactor"></a> <h3 class="subHeader">B-factor Coloring</h3></a> <p> Atomic B-factor values are read from PDB and mmCIF input files and assigned as <a href="/chimerax/docs/user/attributes.html">attributes</a> that can be shown with <a href="/chimerax/docs/user/commands/color.html#byattribute">coloring</a> and used in <a href="/chimerax/docs/user/commands/atomspec.html#attributes">atom specification</a>. This example shows B-factor variation within a structure of the HIV-1 protease bound to an inhibitor (PDB <a href="https://www.rcsb.org/structure/4HVP" target="_blank">4hvp</a>). For complete image setup, including positioning, <a href="/chimerax/docs/user/tools/colorkey.html">color key</a>, and label, see the command file <a href="gallery_samples/bfactor.cxc">bfactor.cxc</a>. </p><p> Additional color key examples can be found in tutorials: <a href="/chimerax/docs/user/tutorials/binding-sites.html#esp">Coloring by Electrostatic Potential</a>, <a href="https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html#omp">Coloring by Sequence Conservation</a> </p><p> <span class="more"><a href="/chimerax/gallery.html">More images...</a></span> </p> </div> <hr class="more"/> </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. 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