Interaction between components

Viewers

As of the current release, Sirius contains three components: structure visualization component, sequence viewer and structure browser component. When the desktop application is started, structure viewer is the displayed by default. If desired, sequence and/or structure browser can be shown as well by choosing the corresponding option in the Viewers menu. Data Access panel also provides an interface for running BLAST in the Uniprot database and access InterPro records.

Sequence Viewer

When a protein structure is loaded in the 3D graphics window, the corresponding amino acid sequence is extracted and displayed in the sequence viewer. Both components are tightly coupled: a selection or coloring event in one of them triggers the same change in the other one. Thus, selecting a residue in the sequence viewer highlights it in the structure display. This interaction can be disabled in the Preferences dialog, but is enabled by default.

Structure Browser

This panel can be a convenient navigation tool, since it's selection is coupled with selection in both 3D and sequence viewers. In addition, it provides a view of the internal structure of the data, whether it's a protein or a small molecule. Right-clicking on each item in the tree view brings up a popup menu with the most commonly used options. Menu items differ for chains, residues and atoms. For example, a chain-specific menu is a quick route to showing a ribbon diagram, while renaming an atom or residue can be easily done through their corresponding menu items. In addition, Structure Browser features an Information Viewer, which is a small panel that is open via a popup menu. It displays basic information about the corresponding structure component, such as name, element (for atoms), position in the chain, classification (amino acid or ligand), etc.

Data access panel

If the database access component is displayed, clicking a structure in the 3D display window or selecting a sequence in the sequence viewer will display the name of the chosen entry in the query text field of the component. If a search is requested, the selected entry will be used as a query. For more specifics about the database access components, refer to the corresponding section.