Sirius visualization software: Difference between revisions

Revision as of 15:34, 17 June 2021

Latest revision as of 21:01, 11 December 2023

(6 intermediate revisions by 4 users not shown)

Line 4:

| 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}}

Line 9 ⟶ 10:

| 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 ==

Line 21 ⟶ 24:

* 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

Line 28 ⟶ 31:

* 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.istoday/20121214224327/http://mbt.sdsc.edu/ |date=2012-12-14 }}</ref>

== RasMol-compatible scripting ==

Line 41 ⟶ 44:

== 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 ==

Line 59 ⟶ 62:

== External links ==

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

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

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

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

* [https://archive.is/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]