Creating animation from 3D visualizations

Loading Molecular Dynamics simulation results

Loading molecular dynamics simulation results that contain time evolution of molecular and atomic structures is similar to what we saw in the previous section, but you need to load two separate files usually that contain the structure itself and another file for movements of the atoms.
Here first we load the molecular structure file, called ubiquitin.psf then we load the movements called pulling.dcd.

In the previous section, we learned how to use and change the graphical representations toolbar. Here we combine multiple graphical representations by using Create Rep and will make one of them Transparent to visualize both of them at the same time.
Also, we are interested to just visualize the main molecular structure without water molecules, so we will use the Selection toolbar to remove water molecules from the visualization.

In order to create animation: Extensions ----> Visualization ----> Movie Maker

First you need to define your rendering engine, similar to what we saw in the previous section at Renderer.
Then you need to define your settings at Movie Settings: For molecular dynamics visualizations it's possible to use Trajectory mode, but for static atomic structures you can rotate the camera by choosing Rotation about Y axis, etc.
Also if you want to keep the images or snapshots at each time frame, uncheck Delete image files.
At the Format section, choose the format of image or movie that you want to create here.
Set Working Directory: Set the path of the files to be generated by this movie maker tool.

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