Data loading and saving

Sirius supports the following structure formats: PDB, MOL2, mmCIF and SDF. Both PDB and SDF files can contain multiple structure entries (PDB NMR models or multiple small molecule entries of SDF files). Sequence formats include ALN and FASTA.

Files with a single structure entry are loaded directly into the viewer as soon as selection is made in the file loading dialog. In the event of multi-model PDB files or SDF files, a file navigator panel is displayed, which lists the contents of the file and allows the user to load any or all of the entries into the workspace. The currently loaded entries are marked red in the list.

Loading of individual models from a 1X26 entry from the Protein Data Bank. Color of consequently loaded structures can be set to either coloring by element (the default) or to a set of different colors that help distinguish one structure from another. These colors can be set in Preferences -> Other.

Sirius also has an option to disable resetting structure view when additional structures are loaded. In this case, the user can find a good view of the structure/complex, and then load one model or structure after another with the entire system keeping the same position. This option is available through the View menu.

Sequence alignment files with multiple individual sequences are regarded as single entries, and can be loaded/closed/saved as a single entity.

Structures can be saved either in their entirety or only their selected parts. Both options are available from the File menu. In addition to structures or sequences, an image of the 3D display can be saved as a PNG or JPG file in resolutions ranging from screen to 300 dpi.

Current state of the display can also be exported as a binary file. It stores all information about the loaded structures or sequences, position of the structures in 3D, their coloring, rendering, ribbon display, distance markers, etc. With this information, the entire view can be restored from the state file.

File Menu Options