TUTORIAL B6 - SECTION 8
Using Sirius with AMBER
By Sasha Buzko
8) Exporting a video of the loaded trajectory and ray-traced frame snapshots
Sirius has several ways to export visual information: video for MD trajectories and still imagery for individual views, which is available in standard rendering quality by Sirius itself and ray-traced photo-quality done by a bundled copy of POV-Ray.
As an example, we will use a trajectory that we looked at in tutorial 3, and the files needed for this exercise are TC5b.prmtop and heat1.mdcrd.gz. Make sure the workspace is cleared, then load the prmtop file followed by the gzipped mdcrd. For visual clarity, show ribbon for the peptide using Appearance->Show/hide ribbon... option in the main application window. You may use the quality slider to set ribbon quality level to 2. This should be sufficient for illustration purposes, although you may want to increase quality more when creating presentation materials (it will increase export time). To add an additional visual element, add a distance measurement from an atom at the N-terminus to another atom at the C-terminal part of the peptide.
With this setup, select Export trajectory as video... from the File menu of the MD panel. You have an option to export a part of the trajectory or the entire loaded run. For this example, let's export the entire run (200 frames). You can select the frame rate (per second of video time). The default (10 fps) provides an interactive experience, while allowing some time to observe changes in the structure. Finally, specify the output file with extension MOV, since the saved video is in QuickTime format.
Once you hit OK, frame-by-frame video export will start and a Processing... message will appear. Once it's gone, the video file is ready to be viewed. The sample exported video can be downloaded here. Experiment with different display options: coloring and rendering individual residues, etc. These options are particularly useful when the focus of the movie is on a particular part of the structure and perhaps a few key residues that need to be highlighted.
To illustrate still image export, let's use a different structure: step1.out.gz. Clear the workspace and load this file. Display a ribbon by selecting Appearance->Show/hide ribbon... Leave ribbon quality setting at its default value and select MOL from the Select structure pulldown menu. Click OK. Next, set mouse selection level to Residue in Selection->Mouse pick selection level in the main application window. Select several residues holding Ctrl key. Then change their rendering mode to stick - use Structure rendering option in the Appearance menu and select Stick as Rendering style when leaving all other options at their default values. Make sure the residues are still selected. Finally, open Show/hide structure dialog in the Appearance menu. Select Show only under Visibility options and click OK. The displayed structure will look similar to the screenshot below.
Next, select Create ray-traced image... from the File menu of the main Sirius window. A small dialog window will appear with the width and height of the desired image in pixels. You can set the dimensions to any values, however keep in mind that very high resolutions dramatically increase memory overhead and image export time. Once you click OK, POV-Ray is activated in the background. Scene rendering can take from 10 seconds to a minute depending on the hardware. Once the processing is completed, the finished image is displayed in a panel next to the main window. Now you will have an option to save the image as a PNG or JPG file. Any subsequent exports will refresh the image in this panel, so there is no need to close it if you are working to optimize the view. The exported image from the sample scene is shown below.
Appearance of the rendered ribbon can be improved by setting ribbon quality to a higher value. Keep in mind that this will increase rendering time due to a larger number of polygons necessary to represent the surface.
Note to Windows users: the very first time ray-traced image is exported, a POV-Ray welcome screen will be displayed. Just click OK and rendering will resume.
Note to MacOS X users: as of current Sirius version (1.1), there is no ray-tracing support for MacOS X. We hope to add it in a few months.
Finally: still images can also be exported directly from Sirius by selecting Export an image... from the File menu. You will only need to specify desired resolution and the output file.
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