Sirius visualization software

Sirius is a molecular modeling and analysis system developed 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
 * Command line interpreter and scripting support fully compatible with existing RasMol scripts
 * 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.

RasMol-compatible scripting
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 existing scripts. Additional commands introduced in Sirius have been added to provide support for manipulation of multiple structures loaded at the same time, and to enable more flexible selection.

Existing 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. For details, refer to Sirius help.

Sirius supports a number of predefined atom/residue sets and color schemes, as well as allows for editing of scripts using the Command Panel interface. In addition, logical operators and parentheses can be used to create complex selection commands.

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.