TUTORIAL B6 - SECTION 6
Using Sirius with AMBER
By Sasha Buzko
6) Advanced visualization options
A. Displaying solvent
Simulations are frequently carried out with explicit solvent molecules, which adds a considerable loading and playback overhead. If you wish to view the complete simulation along with solvent molecules, no special action is required - everything is shown by default. If, however, you would like to omit solvent loading altogether and see only the solute, you can use Do not load solvent option in the Data menu of the MD panel.
For this example, load polyAT_wat.prmtop and polyAT_wat_md1.mdcrd.gz. It may take a few seconds to load the first frame, after which you will see a fragment of DNA within a bounding box of water molecules. The entire set contains 9560 atoms.
Now clear the display and select Do not load solvent in the Data menu. Load the same prmtop and mdcrd files. Only the DNA and other ions are displayed, while water molecules are skipped during the loading process. The total number of loaded atoms now is only 656. With this representation, you can practice with rendering and coloring options. For example, you can select all sodium atoms by clicking Select by element... in the Selection menu of the main window. When you click an element in the periodic table, the corresponding atoms are selected. Once Na atoms are highlighted, choose Structure rendering... from the Appearance menu and set style to ball-and-stick leaving Apply to at Currently selected. The resulting view is in the screenshot below.
Depending on your hardware, loading with no solvent may also produce a much more interactive playback for very large systems.
B. View centering
Sometimes position of the structure shifts considerably during simulations and disappears from the view. This may force you to reset view several times during the simulation (View->Reset view). However, even this doesn't solve the problem if a video export is needed.
This type of issue is fixed by enabling Keep view centered option in the Data menu of the MD panel. Once this setting is enabled, the view will adjust at every frame to keep the entire structure visible. For this exersize you will need the following files: 3k1.vac.prmtop and 3k.tip4p.mdcrd.gz.
Open Molecular Dynamics panel, then select Open parameter file from the File menu. Select the 3k1.vac.prmtop file and load it. Then load the trajectory from 3k.tip4p.mdcrd.gz. A short peptide will appear. For easier observation, compute the RMSD graph for the trajectory as described in the previous section. Leave the settings at their default values and generate the graph.
Since the trajectory is relatively long (1000 frames), increase the speed of playback. Now run the trajectory with default settings, simply by clicking Play. At approximately frame 200, the structure will disappear and will be seen only partially throughout the trajectory.
Now, click Reset on the control panel, and enable view centering by clicking "Keep view centered" under the Data menu. Replay the trajectory. With the centering enabled, the structure remains entirely within the view.
C. Secondary structure update
In simulations that model protein folding it is advantageous to see when the structure begins adopting conformations close to those of ordered helices or strands. These are best highlighted by rendered ribbons with specific color corresponding to each secondary structure type. Sirius also supports dynamic updates of secondary structure, which allows you to monitor changes in peptide conformation.
To illustrate this feature, you will need the following two files: helix.prmtop and helix.mdcrd.gz. Load the prmtop file and the gzipped trajectory. Once the entire trajectory is loaded, the frame count should be 2290. Then, in the Data menu of the MD panel, enable option Real-time secondary structure update. To show the existing secondary structure, select Appearance->Show/hide ribbon menu item in the main Sirius window. Click the loaded peptide structure or select its name from the pulldown menu at the bottom of the Apply to panel. Then choose ribbon type to be Round cross-section and click ok. You will see a linear peptide with a blue-colored ribbon denoting a non-specific coil.
Next, start playback of the trajectory. As the display progresses through the frames, the spatial arrangement of the residues is analyzed. Once a fragment of the loaded peptide begins to fold into a helix, the corresponding part of the ribbon is colored red. A sample frame from the trajectory is shown in the image below.
Specific color scheme for secondary structure elements (helix, strand, etc.) can be specified in the Preferences dialog (under Tools menu) in the Structure Viewer tab.
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