TUTORIAL B6 - SECTION 2
Using Sirius with AMBER
By Sasha Buzko
2) Loading structures from PDB and local files
With Sirius open, structures can be loaded directly from the PDB by selecting Load from PDB... option under the File menu. Alternatively, the corresponding buttonin the toolbar on the left can be used. A dialog box then requests the PDB id and with that information the structure is loaded. For example, type 102m into the text field of the loader dialog and hit Enter or click OK button. The corresponding structure of hemoglobin will be loaded. Structures are removed from the 3D workspace by selecting File->Close entry or Close all entries.
In addition to the 3D view, the sequence viewer can be open via the Tools menu to display the primary amino acid sequence.
For example, type 102m into the PDB loader dialog and hit Enter or click OK button. The corresponding structure of a hemoglobin will be loaded. Structures are manipulated using mouse buttons. Hold the left (primary) button and drag the mouse for free rotation, hold the right button and drag for translation within the screen plane. In order to zoom in or out, use the middle button or a mouse wheel. If your mouse has no wheel or middle button, press and hold Alt key while holding the left mouse button. This substitution for a middle button/wheel is set in the Preferences dialog and is enabled by default.
Secondary structure can be visualized using ribbon display. To add a ribbon, select Show/hide ribbon... option from the Appearance menu. You can set quality level with a slider, as well as specify which chain in the structure the ribbon should be shown for. Leave quality slider at the default setting and select "102m" from the pulldown menu to apply the ribbon display to the entire structure and click OK.
In order to see hierarchical structure of the data, you can use Structure Browser, which is accessed via the Viewers menu. Structure Browser is a panel that shows all loaded structures, with their chains, residues and atoms in a tree-like fashion. Selecting an element in the Browser highlights the corresponding component in the 3D workspace. Click "Chain C" that corresponds to the heme ligand and the corresponding part of the structure becomes highlighted.
Sirius allows for setting different rendering for any part of the structure independently from others. The rendering dialog (under Appearance menu or a separate button in Structure Browser) can be used to apply various rendering types (line, stick, ball-stick and space-filling) to either the entire structure, a chain, a residue or individual atom that was picked by the mouse. To practice, with the heme residue selected, click Render button in the Structure Browser and choose ball and stick as the rendering style. Keep "Apply to" option at "Currently selected" and change quality to Best. This will change appearance of the heme to ball and stick. You could also apply selected style to any residue by picking it with the mouse and choosing Residue option.
Structures can also be loaded from the local filesystem using the Open file... option under the File menu or in the toolbar. Choose the file type using the pulldown menu in the dialog and select the desired file. The structure is then loaded in the same manner as the remotely retrieved PDB file. Currently supported file formats are PDB, MOL2, SDF/MOL, mmCIF. Sequences can be loaded in CLUSTALW aln, MSF and FASTA formats. As of version 1.2, GAMESS input files and RasMol scripts can also be imported.
An advanced display concept: For better depth perception, a fog effect is introduced in the 3D scene. It makes more distant objects appear more blended into the background (darker for black background). There are two distance values: front fog plane and back fog plane. The front plane determines where any fog is added to the scene, i.e. anything closer than this distance appears in pure color. The back plane is the position beyond which everything is black. Ideally, the front plane should be immediately before the protein structure, and the back plane immediately after it. This way, the depth will be optimal. To adjust it, use Set depth perception... option under View menu. Sliders can be used to adjust position of both fog planes with real time feedback in the display.
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