Screenshots

Sirius is shown with a structure of protein kinase CDK2 and open BLAST panel. Similar sequences are loaded in the viewer from the Uniprot database. Common selection across viewers produces an easy reference on location of any given amino acid residue.

A structure of a protein fragment is loaded and instramolecular hydrogen bonds are detected. In addition, several distance and label elements are shown. The display elements can be managed via the visual interface using a hierarchical structure.

A screenshot of a molecular dynamics trajectory loaded using the MD Panel. Real-time display of RMSD can be computed for any subset of atoms of the loaded structure, and entering frame number or dragging the slider enable fast navigation to the desired location within the trajectory. Molecular Dynamics panel reads AMBER and CHARMM output files, including those with charge and bounding box information. Sirius also can load concatenated PDB files.

New structures can be built from the provided fragment palette by clicking hydrogen atoms where the new fragment should be added. The structure can be further edited by rotating groups around bonds, changing elements, hybridization or bond order. Fragments also support alternative attachment points.

Sirius is distributed with a bundled copy of POV-Ray, a ray-tracing software capable of creating photo-realistic graphics. On Windows and Linux, a rendered image can be created directly from the loaded 3D scene and displayed in an image preview panel. The image shown was created on Linux using a structure of hemoglobin (PDB id 102m). MacOS X users can still use this feature, although it is restricted to saving a POV-Ray input file that has to be run through an interactive session of POV-Ray separately.

Sirius offers full support for scripting and command-line based manipulation of rendering, visibility, coloring, ribbon display, orientation, etc. It is also compatible with existing RasMol scripts. The image above was created by loading a RasMol script and exporting the 3D view as a high-resolution image.