Sirius visualization software: Difference between revisions

Revision as of 09:54, 29 December 2016

Latest revision as of 21:01, 11 December 2023

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

| developer = San Diego Supercomputer Center

| discontinued = yes

| latest release version = 1.2

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

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| genre = [[Molecular modelling]]

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

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

}}

'''Sirius''' is a [[molecular modelling]] and analysis system developed 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. Sirius supports high quality interactive [[3D graphics]], structure building, displaying [[protein]] or [[DNA]] [[primary sequence]]s, access to remote data sources, and visualizing [[molecular dynamics]] trajectories. It can be used for [[scientific visualization]] and analysis, and [[chemistry]] and [[biology]] instruction.

This software is no longer supported as of 2011.

== Key features ==

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

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

* [[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

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* Integrated selection and coloring across individual visualizing 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 ==

<!-- 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 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>

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== Visualizing molecular dynamics trajectories ==

Sirius contains a full-featured molecular dynamics (MD) visualizing component. It can read output files from [[AMBER]] and [[CHARMM]] simulations, including compressed and AMBER out files. [[RMSD]] 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 [[protein]] fold, Sirius can 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.

== Access 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]]. 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].

== See also ==

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* [[Molecular graphics]]

* [[Molecular dynamics]]

==References==

{{Reflist}}

== External links ==

* [https://web.archive.org/web/20110406034756/http://sirius.sdsc.edu/ Internet Archive of Official Website]

* {{Official website|sirius.sdsc.edu}}

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

* [http://sirius.sdsc.edu/tutorial/tutorials.html Sirius tutorials]

* [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]]