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<span id="openzim-page-title" class="mw-page-title-main"><span class="mw-page-title-main">Sirius visualization software</span></span>
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</style><table class="infobox vevent"><tbody><tr><th colspan="2" class="infobox-above summary">Sirius</th></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Programmer" title="Programmer">Developer(s)</a></th><td class="infobox-data">San Diego Supercomputer Center</td></tr><tr style="display: none;"><td colspan="2" class="infobox-full-data"></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_release_life_cycle" title="Software release life cycle">Final release</a></th><td class="infobox-data"><div style="margin:0px;">1.2
/ November 18, 2008<span style="display:none"> (<span class="bday dtstart published updated">2008-11-18</span>)</span></div></td></tr><tr style="display:none"><td colspan="2">
</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Operating_system" title="Operating system">Operating system</a></th><td class="infobox-data"><a href="Cross-platform" class="mw-redirect" title="Cross-platform">Cross-platform</a>: <a href="Microsoft_Windows" title="Microsoft Windows">Windows</a>, <a href="Linux" title="Linux">Linux</a>, <a href="MacOS" title="MacOS">macOS</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_categories#Categorization_approaches" title="Software categories">Type</a></th><td class="infobox-data"><a href="Molecular_modelling" title="Molecular modelling">Molecular modelling</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_license" title="Software license">License</a></th><td class="infobox-data"><a href="Proprietary_software" title="Proprietary software">Proprietary</a> <a href="Freeware" title="Freeware">freeware</a> for academic, non-profit</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Website</th><td class="infobox-data"><span class="url"><a rel="nofollow" class="external text" href="https://web.archive.org/web/20110406034756/http://sirius.sdsc.edu/">web<wbr>.archive<wbr>.org<wbr>/web<wbr>/20110406034756<wbr>/http:<wbr>//sirius<wbr>.sdsc<wbr>.edu<wbr>/</a></span></td></tr></tbody></table>
<p><b>Sirius</b> is a <a href="Molecular_modelling" title="Molecular modelling">molecular modelling</a> and analysis system developed at <a href="San_Diego_Supercomputer_Center" title="San Diego Supercomputer Center">San Diego Supercomputer Center</a>. Sirius is designed to support advanced user requirements that go beyond simple display of small <a href="Molecule" title="Molecule">molecules</a> and <a href="Protein" title="Protein">proteins</a>. Sirius supports high quality interactive <a href="3D_graphics" class="mw-redirect" title="3D graphics">3D graphics</a>, structure building, displaying <a href="Protein" title="Protein">protein</a> or <a href="DNA" title="DNA">DNA</a> <a href="Primary_sequence" class="mw-redirect" title="Primary sequence">primary sequences</a>, access to remote data sources, and visualizing <a href="Molecular_dynamics" title="Molecular dynamics">molecular dynamics</a> trajectories. It can be used for <a href="Scientific_visualization" title="Scientific visualization">scientific visualization</a> and analysis, and <a href="Chemistry" title="Chemistry">chemistry</a> and <a href="Biology" title="Biology">biology</a> instruction.
</p><p>This software is no longer supported as of 2011.
</p>
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<div class="mw-heading mw-heading2"><h2 id="Key_features">Key features</h2></div>
<p>Sirius supports a variety of applications with a set of features, including:
</p>
<ul><li>Building and editing chemical structures using a library of fragments</li>
<li>Protein structure and <a href="Sequence_alignment" title="Sequence alignment">sequence alignment</a></li>
<li>Command line interpreter and scripting support fully compatible with extant <a href="RasMol" title="RasMol">RasMol</a> scripts</li>
<li>Full support for <a href="Molecular_dynamics" title="Molecular dynamics">molecular dynamics</a> trajectory visualizing</li>
<li><a href="BLAST_(biotechnology)" title="BLAST (biotechnology)">BLAST</a> search directly in <a href="Protein_Data_Bank" title="Protein Data Bank">Protein Data Bank</a> and <a href="Uniprot" class="mw-redirect" title="Uniprot">Uniprot</a> databases</li>
<li>Ability to move parts of the loaded data while freezing the rest</li>
<li>Interactive calculation of <a href="Hydrogen_bond" title="Hydrogen bond">hydrogen bonding</a>, steric clashes, <a href="Ramachandran_plot" title="Ramachandran plot">Ramachandran plots</a></li>
<li>Support for all major structure and sequence formats</li>
<li>Bundled <a href="POV-Ray" title="POV-Ray">POV-Ray</a> for creating photorealistic images</li>
<li>Integrated selection and coloring across individual visualizing components</li></ul>
<p>Sirius is based on molecular graphics code and data structures developed as a part of the Molecular Biology Toolkit.<sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup>
</p>
<div class="mw-heading mw-heading2"><h2 id="RasMol-compatible_scripting">RasMol-compatible scripting</h2></div>
<p>Sirius features a command line interpreter that can be used to quickly manipulate structure appearance and orientation. The set of commands has been patterned after <a href="RasMol" title="RasMol">RasMol</a>, so it's fully compatible with extant scripts. Added commands introduced in Sirius provide support for manipulating multiple structures loaded at the same time, and enable more flexible selection.
</p><p>Extant RasMol scripts can be imported and run within Sirius to produce high quality representations of encoded molecular scenes. Since RasMol uses a coordinate system that differs from that Sirius, internal conversion is performed when RasMol scripts are imported, so that any orientation changes are shown correctly. Any manually entered commands, however, are executed according to the Sirius coordinate system.<sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup>
</p><p>Sirius supports several predefined atom-residue sets and color schemes, allows editing of scripts using the Command Panel interface, and logical operators and parentheses can be used to create complex selection commands.
</p>
<div class="mw-heading mw-heading2"><h2 id="Visualizing_molecular_dynamics_trajectories">Visualizing molecular dynamics trajectories</h2></div>
<p>Sirius contains a full-featured molecular dynamics visualizing component. It can read output files from <a href="AMBER" title="AMBER">AMBER</a> and <a href="CHARMM" title="CHARMM">CHARMM</a> simulations, including compressed and AMBER out files. <a href="RMSD" class="mw-redirect" title="RMSD">RMSD</a> changes along the trajectory can be calculated using user-defined atom subsets and displayed in an interactively updated graph. In order to reduce memory requirements, large multifile simulations may be loaded in a buffered mode. If a simulation involves changes in <a href="Protein" title="Protein">protein</a> fold, Sirius can be set to track and recompute displayed <a href="Secondary_structure" class="mw-redirect" title="Secondary structure">secondary structure</a> features in real time, which provides a convenient way to observe transformations of the structure. The full trajectory or selected frames can be exported as <a href="QuickTime" title="QuickTime">QuickTime</a> video or a set of <a href="POV-Ray" title="POV-Ray">POV-Ray</a> scene snapshots that can later be converted to a high quality movie.
</p>
<div class="mw-heading mw-heading2"><h2 id="Access_and_download">Access and download</h2></div>
<p>Sirius is distributed freely from the project website to individuals affiliated with academic and non-profit organizations.<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> Native desktop application installers are available for <a href="Microsoft_Windows" title="Microsoft Windows">Windows</a>, <a href="Linux" title="Linux">Linux</a>, and <a href="MacOS" title="MacOS">macOS</a>.
</p>
<div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2></div>
<ul><li><a href="Comparison_of_software_for_molecular_mechanics_modeling" title="Comparison of software for molecular mechanics modeling">Comparison of software for molecular mechanics modeling</a></li>
<li><a href="List_of_molecular_graphics_systems" title="List of molecular graphics systems">List of molecular graphics systems</a></li>
<li><a href="Molecule_editor" title="Molecule editor">Molecule editor</a></li>
<li><a href="Molecular_modelling" title="Molecular modelling">Molecular modelling</a></li>
<li><a href="Molecular_graphics" title="Molecular graphics">Molecular graphics</a></li>
<li><a href="Molecular_dynamics" title="Molecular dynamics">Molecular dynamics</a></li></ul>
<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>
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<div class="mw-references-wrap"><ol class="references">
<li id="cite_note-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-1">^</a></b></span> <span class="reference-text"><a rel="nofollow" class="external text" href="http://mbt.sdsc.edu">Molecular Biology Toolkit</a> <a rel="nofollow" class="external text" href="https://archive.today/20121214224327/http://mbt.sdsc.edu/">Archived</a> 2012-12-14 at <a href="Archive.today" title="Archive.today">archive.today</a></span>
</li>
<li id="cite_note-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-2">^</a></b></span> <span class="reference-text"><a rel="nofollow" class="external text" href="http://sirius.sdsc.edu/help">Sirius help</a></span>
</li>
<li id="cite_note-3"><span class="mw-cite-backlink"><b><a href="#cite_ref-3">^</a></b></span> <span class="reference-text"><a rel="nofollow" class="external text" href="http://sirius.sdsc.edu/downloads.php">Sirius downloads</a></span>
</li>
</ol></div></div>
<div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2></div>
<ul><li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20110406034756/http://sirius.sdsc.edu/">Internet Archive of Official Website</a></li>
<li><a rel="nofollow" class="external text" href="https://archive.today/20121214224327/http://mbt.sdsc.edu/">Molecular Biology Toolkit</a></li>
<li><a rel="nofollow" class="external text" href="http://www.sdsc.edu">San Diego Supercomputer Center</a></li>
<li><a rel="nofollow" class="external text" href="http://www.ucsd.edu">University of California San Diego</a></li></ul></div><!--htdig_noindex--><div><div class="zim-footer">
This article is issued from <a class="external text" title="Last edited on 2023-12-11" href="https://en.wikipedia.org/wiki/?title=Sirius_visualization_software&oldid=1189439397">Wikipedia</a>. The text is available under <a class="external text" href="https://creativecommons.org/licenses/by-sa/4.0/deed.en">Creative Commons Attribution-Share Alike 4.0</a> unless otherwise noted. Additional terms may apply for the media files.
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