Making quick 3D movies with PyMOL

We demonstrate how to obtain simple 3D movies of molecules by picturing at different molecular orientations.

First of all, open the PyMOL Zalman® 3D program, and then open the .pdb file, or .pse file containing your molecule of interest. After that, change the style of representation and color as you wish from the right panel. Then select the Stereo menu item from the Display menu. The Scene selection buttons can be added by selecting the Button menu item from the Scene menu. At this point, you can add a scene by moving the molecule to the final orientation for the new scene, then select the Append menu item from Scene menu. PyMOL will automatically compute the transformation necessary to create a scene depicting the orientation change. Repeat the steps of appending scenes as desired. It should be noted that rendering a movie for 3 scenes could take up to an hour on a high-end workstation. When a molecule has moved into its final orientation of each scene, additional effects can be added. For example, a molecule can be shown swaying around the axis pointing towards the viewer for 4 seconds before starting the next scene. To add such an effect, select the Program menu item under the Movie menu and then select the Nutate option under the Scene Loop. The movie can be seen by clicking on the Play button. After this step, a movie with 3D capability can be created in different ways. In this paper, we will outline 2 methods, which are easy to execute.

The first method for creating a movie is by exporting a PyMOL movie into series of PNG images, i.e. selecting “Save movie as” from the PyMOL Zalman® 3D File menu. Then, these PNG images can be stitched together to create a MOV movie using the FFmpeg-0.10.3 program through a command line interface. Below is an example of a command to create a movie file named from the files img_xxxx.png in the same directory.

ffmpeg -sameq -r 60 -i img_%04d.png -y

Alternatively, a movie can also be recorded by a screen capturing program such as SnagIt. Both methods can preserve the 3D capability as long as the user activates the Zalman® 3D stereo option without turning on the face tracking system through 3D Screen Activator. While playing this movie file, turning on the Full Screen Mode will preserve the screen resolution for the 3D display. The movie can be viewed in 3D full screen mode on a Zalman® display or on Toshiba® Qosmio F750-3D with a 3D Screen Activator. For advanced movie creation methods, please consult PyMOL Wiki.

Click here to see the Staurosporine Environment rendered in row-interleaved format for both glasses free 3D display and passive stereoscopic display.

Source: Tanramluk D, Akavipat R, Charoensawan V, Toward mobile 3D visualization for structural biologists. Mol. BioSyst., 2013, 9 (12), 2956 – 2960.


About nanonan

Bioinformaticist and Structural Biologist
This entry was posted in 3D movie, 3D visualisation, autostereoscopic, passive stereoscopic, PyMOL, row interleaved. Bookmark the permalink.

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