Sirius visualization software: Difference between revisions

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{{Infobox Software |software

| name = Sirius |

| screenshot = <!-- Commented out because image was deleted: [[Image:Sirius_large.png|275px]] |-->

| caption = Sirius running with structure browser and sequence viewer open. Displayed, isdisplaying hemoglobin (PDB id 102m). |

| developer = San Diego Supercomputer Center |

| discontinued = yes

latest_release_version = 1.1 |

| latest release version = 1.2

latest_release_date = [[May 3]], [[2007]] |

| latest release date = {{Start date and age|2008|11|18}}

operating_system = many |

| operating system = [[Cross-platform]]: [[Microsoft Windows|Windows]], [[Linux]], [[macOS]]

| genre = [[Molecular modelling]] |

license = free for academic/non-profit |

| license = [[Proprietary software|Proprietary]] [[freeware]] for academic, non-profit

website = [http://sirius.sdsc.edu sirius.sdsc.edu] |

| website = {{URL|https://web.archive.org/web/20110406034756/http://sirius.sdsc.edu/}}

}}

'''Sirius''' is a [[molecular modelingmodelling]] and analysis system developed by Oleksandr (Sasha) Buzko at [[San Diego Supercomputer Center]]. Sirius is designed to support advanced user requirements that go beyond simple display of small [[molecule]]s and [[protein]]s. InSirius addition tosupports high quality interactive [[3D graphics]], Sirius supports structure building, displaying [[protein]] or [[DNA]] [[primary sequence]]s, access to remote data sources, and visualization ofvisualizing [[molecular dynamics]] trajectories. SiriusIt can be used for [[scientific visualization]] and analysis, as well as forand [[chemistry]] and [[biology]] instruction.

This software is no longer supported as of 2011.

== The key features ==

== Key features ==

Sirius supports a variety of applications with a set of features, that includeincluding:

* Building and editing chemical structures using a library of fragments

* Protein structure and [[sequence alignment]]

* Command line interpreter and scripting support fully compatible with extant [[RasMol]] scripts

* Full support for [[molecular dynamics]] trajectory visualizationvisualizing

* [[BLAST (biotechnology)|BLAST]] search directly in [[Protein Data Bank]] and [[Uniprot]] databases

* Ability to move parts of the loaded data while freezing the rest

* Interactive calculation of [[hydrogen bond]]ing, steric clashes, [[Ramachandran plot]]s

* Support for all major structure and sequence formats

* Bundled [[POV-Ray]] for creating photorealistic images

* Integrated selection and coloring across individual visualizationvisualizing components

Sirius is based on molecular graphics code and data structures developed as a part of the Molecular Biology Toolkit.<ref>[http://mbt.sdsc.edu Molecular Biology Toolkit] {{webarchive|url=https://archive.today/20121214224327/http://mbt.sdsc.edu/ |date=2012-12-14 }}</ref>

== RasMol-compatible scripting ==

== Visualization of molecular dynamics trajectories ==

<!-- Commented out because image was deleted: [[Image:Sirius_rasmol_import.png|right|thumb|275px|Image of a molecular scene encoded by a RasMol script. Created using Sirius.]] -->

Sirius contains a full-featured molecular dynamics (MD) visualization component. It can read output files from [[AMBER]] and [[CHARMM]] simulations, including compressed and AMBER output files. [[RMSD]] change 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 [[protein]] fold, Sirius may be set to track and recompute displayed [[secondary structure]] 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 [[QuickTime]] video.

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 [[RasMol]], 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.

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.<ref>[http://sirius.sdsc.edu/help Sirius help]</ref>

== Sirius access and download ==

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.

Sirius is distributed freely from the project [http://sirius.sdsc.edu/downloads.php website] to individuals affiliated with academic and non-profit organizations. Native desktop application installers are available for [[Windows]], [[Linux]] and [[Mac OS X]]. In addition to providing the downloads, the project site contains Sirius [http://sirius.sdsc.edu/help help system], [http://sirius.sdsc.edu/tutorial/tutorials.html tutorials] and [http://sirius.sdsc.edu/screenshots.php screenshots].

== Visualization ofVisualizing molecular dynamics trajectories ==

== See also ==

Sirius contains a full-featured molecular dynamics (MD) visualizationvisualizing component. It can read output files from [[AMBER]] and [[CHARMM]] simulations, including compressed and AMBER outputout files. [[RMSD]] changechanges 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 [[protein]] fold, Sirius maycan be set to track and recompute displayed [[secondary structure]] 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 [[QuickTime]] video or a set of [[POV-Ray]] scene snapshots that can later be converted to a high quality movie.

== Sirius accessAccess and download ==

Sirius is distributed freely from the project website to individuals affiliated with academic and non-profit organizations.<ref>[http://sirius.sdsc.edu/downloads.php Sirius downloads]</ref> Native desktop application installers are available for [[Microsoft Windows|Windows]], [[Linux]], and [[macOS]].

== See also ==

* [[Comparison of software for molecular mechanics modeling]]

* [[List of molecular graphics systems]]

* [[Molecule editor]]

* [[Molecular modelling]]

* [[Molecular graphics]]

* [[Molecular dynamics]]

==References==

== External links ==

{{Reflist}}

== External links ==

* [http://sirius.sdsc.edu Sirius Home Page]

* [https://web.archive.org/web/20110406034756/http://sirius.sdsc.edu/tutorial/tutorials.html SiriusInternet Archive of Official tutorialsWebsite]

* [https://archive.today/20121214224327/http://mbt.sdsc.edu/ Molecular Biology Toolkit]

* [http://www.sdsc.edu San Diego Supercomputer Center]

* [http://www.ucsd.edu University of California San Diego]

[[Category:Molecular modelling software]]

[[Category:Bioinformatics software]]

[[Category:Free science software]]