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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://www.nature.com/articles/s41586-025-08773-x" target="_blank"> A coronavirus assembly inhibitor that targets the viral membrane protein.</a> Laporte M, Jochmans D <i>et al.</i> <i>Nature.</i> 2025 Apr 10;640(8058):514–523. </p> <p class="newsItem"> <a href="https://rupress.org/jcb/article/224/4/e202407110/277307/Cytoplasmic-ribosomes-on-mitochondria-alter-the" target="_blank"> Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import.</a> Chang YT, Barad BA <i>et al.</i> <i>J Cell Biol.</i> 2025 Apr 7;224(4):e202407110. </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.science.org/doi/10.1126/sciadv.adt2127" target="_blank"> Structural basis for the pore-forming activity of a complement-like toxin.</a> Johnstone BA, Christie MP <i>et al.</i> <i>Sci Adv.</i> 2025 Mar 28;11(13):eadt2127. </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> <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:325px"> <a href="feature_highlights/mlp.png"> <img src="feature_highlights/mlp.png" width="260px" height="320px" alt="membrane protein with lipophilicity coloring" hspace="15px" title="click to enlarge..." style="float: right;"></a> <a name="mlp"></a> <h3 class="subHeader">Coloring by Molecular Lipophilicity Potential</h3> <p> Molecular lipophilicity potential (MLP) can be calculated for a protein and displayed with surface coloring using the command <a href="/chimerax/docs/user/commands/mlp.html"><b>mlp</b></a> or the <a href="/chimerax/docs/user/tools/moldisplay.html"><b>Molecule Display</b></a> icon <a href="/chimerax/docs/user/tools/moldisplay.html"> <img style="width:20px; margin: 1px -1px; vertical-align:middle; border:1px solid black" src="/chimerax/docs/user/tools/shortcut-icons/hydrophobicity.png"></a>. The image shows the photosynthetic reaction center from a purple sulfur bacterium, with MLP coloring on the molecular surface and membrane boundaries from OPM (Orientations of Proteins in Membranes entry <a href="https://opm.phar.umich.edu/proteins/47" target="_blank">1eys</a>). Blue and red balls represent the cytoplasmic and periplasmic sides of the bacterial inner membrane, respectively. Parts of the L, M, and H chains span the membrane, whereas the cytochrome subunit sits on the periplasmic side, at the top. The surface coloring ranges from dark goldenrod for the most hydrophobic potentials, through white, to dark cyan for the most hydrophilic. Ligands including lipid, detergent, heme, and various other cofactors are shown as purple surfaces. </p><p> For image setup after the structure from OPM has been opened, see the command file <a href="feature_highlights/mlp.cxc">mlp.cxc</a>. </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/cam.png"> <img src="gallery_samples/cam.png" width="300px" height="250px" alt="CaM-CaMKI peptide" hspace="15px" title="click to enlarge..." style="float: right;"></a> <a name="cam"></a> <h3 class="subHeader">Calmodulin and Target Peptide</h3></a> <p> Calmodulin (CaM) acts as a calcium sensor. When its four Ca++ sites are fully occupied, it binds and modulates the activity of various downstream proteins, including CaM-dependent protein kinase I (CaMKI). Here, a complex between CaM and its target peptide from CaMKI (PDB <a href="https://www.rcsb.org/structure/1MXE" target="_blank">1mxe</a>) is shown with cartoons, a transparent molecular surface, silhouette outlines, and <a href="/chimerax/docs/user/commands/lighting.html#preset">light soft</a> ambient occlusion. (If you prefer a less smudgy/rustic appearance, try using <a href="/chimerax/docs/user/commands/lighting.html#preset">light gentle</a> instead.) For image setup other than positioning, see the command file <a href="gallery_samples/cam.cxc">cam.cxc</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. All rights reserved. </font></p> </body></html>