Sirius visualization software
| File:Sirius large.png Sirius running with structure browser and sequence viewer open. Displayed is hemoglobin (PDB id 102m). | |
| Developer(s) | San Diego Supercomputer Center |
|---|---|
| Stable release | |
| Operating system | many |
| Type | Molecular modelling |
| License | free for academic/non-profit |
| Website | sirius.sdsc.edu |
Sirius is a molecular modeling 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 molecules and proteins. In addition to high quality interactive 3D graphics, Sirius supports structure building, displaying protein or DNA primary sequences, access to remote data sources and visualization of molecular dynamics trajectories. Sirius can be used for scientific visualization and analysis, as well as for chemistry and biology instruction.
The key features
Sirius supports a variety of applications with a set of features that include
- Building and editing chemical structures using a library of fragments
- Protein structure and sequence alignment
- Full support for molecular dynamics trajectory visualization
- 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 bonding, steric clashes, Ramachandran plots
- Support for all major structure and sequence formats
- Bundled POV-Ray for creating photorealistic images
- Integrated selection and coloring across individual visualization components
Sirius is based on molecular graphics code and data structures developed as a part of Molecular Biology Toolkit.
Visualization of molecular dynamics trajectories
Sirius contains a full-featured molecular dynamics (MD) visualization 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.
Sirius access and download
Sirius is distributed freely from the project 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 help system, tutorials and screenshots.