Now that we’ve talked about images, it’s also important to discuss making movies. Yep, you read that right–you can save your protein’s wiggles in a video! To do this, follow Extensions → Visualization → Movie Maker in the main menu. This brings up the VMD Movie Generator menu (see the image below).

The VMD movie generator window. The top has 4 drop-down menus, currently listing 'Renderer', 'Movie Settings', 'Format', and 'Help.' Next is a button with 'Set working directory.' Then 4 boxes can be filled in; 'name of movie,' 'rotation angle,' 'trajectory step size', and 'movie duration (status).' Next is progression information. The status is ready, and stage and progress are both 0 of 0. There are two buttons at the bottom: 'Make movie' and 'abort.'
The VMD Movie Generator menu.

The first thing you should do is choose the working directory for making the movie. It’s set as a temp folder by default, which isn’t necessarily a bad thing, but it does mean that your movie will be saved in that temporary directory. So set it to a place you can find it, or just know how to get to that default temp directory. Next, title your film! Make it descriptive so future you knows what system it is and what you’re looking at.

Up in the dropdown menus, the first up is the Renderer. Unlike images, using the Snapshot (screen capture) option is acceptable for movies. However, if you chose this option, it is critical that the VMD window isn’t covered by other windows (or browsers or terminals, etc.) in the process, because otherwise your video will have those landmarks in it. Under Movie Settings, there are two that you’ll likely want to use for movies. The first is Rotation about Y axis–this does exactly like it sounds. The second is Trajectory. This is what will actually save your wiggling protein as a movie. As for format, the default MPEG-1 (ppmtompeg) should be fine, unless you have a strong reason for needing a different format.

The other options, Rotation angle, Trajectory step size, and Movie duration depend on what you’re doing and what you’re making the movie for. The rotation angle specifies how far anything that rotates should. If you’re using Rotation about Y axis to show off your protein, then you probably want that to be 360; if you’re making a trajectory movie then you’ll want it to be 0. Trajectory step size specifies how many frames to skip when making your movie. The larger the step size, the more choppy the video will look, but the shorter it will be. You only can choose to set a trajectory movie based on step size or duration–not both. Typically, people won’t want to watch anything more than a 25 second video played on a loop.

Once you’ve decided all the settings, hit that Make Movie button, making sure that nothing is in the way of the VMD OpenGL Display window (where you are currently looking at the protein), and watch it go.

Success! A video has been made!