Making movies in VMD

Install the ffmpeg encoder

The iMAcs are not well equipped for movie making so we need to install the ffmpeg encoder from http://becksteinlab.physics.asu.edu/pages/courses/2013/SimBioNano/10/ffmpeg/

cd ~/bin
curl -O http://becksteinlab.physics.asu.edu/pages/courses/2013/SimBioNano/10/ffmpeg/ffmpeg
chmod a+x ffmpeg

Then make sure that ffmpeg is found on your PATH:

echo "export PATH=$HOME/bin:$PATH" >> ~/.profile

(You might have to log out and log in for this to have full effect later on.)

AdK transition movie

We use the standard VMD plugin MovieMaker.

1. Load the AdK transition trajectory from Analyzing protein dynamics.

2. Use a nice representation, e.g. color the CORE, LID, and NMP domains. You can also find a number of salt bridges (pairs of basic/positively charged and acidic/negatively charge residues) that “zip up” AdK (see the AdK zipping movie from Beckstein et al).

3. Open Extension -> Visualization -> Movie Maker

4. Settings

   • Renderer: Snapshot (for “Hollywood”-style movies, use one of the ray tracers such as tachyon + AO)
   • Movie Settings: Trajectory
   • Set Format to MPEG-1 (ffmpeg). (MPEG-2 is better but the iMacs can’t display it).
   • Set your working directory to e.g. ~/USERNAME/p10/movies (so that you can easily find the finished movie)
   • Name your movie, e.g. adk_transition.

5. Make Movie: should step through your trajectory, write out frames, and finally run ffmpeg.

6. In the shell, go to your movie directory and play it:

   open adk_transition.mpg

Advanced movie making

In order to rotate and zoom a movie during a trajectory we can use the VMD ViewChangeRender plugin together with MovieMaker.

Open ViewChangeRender Extensions -> Visualization -> ViewChangeRender. Generate “viewpoints” of your movie:

1. Adjust position in trajectory, rotate, zoom.
2. Save Viewpoint

Repeat for as many viewpoints as you want to include.

Add all viewpoints to movie: The final movie will smoothly interpolate between these points. You can check with Preview Movie. (Note that this plugin has a few bugs so you might have to quit and restart when it stops working.)

Once you are ready to render the movie:

1. In ViewChangeRender: Enable
2. In MovieMaker:
   1. Movie Settings: User defined procedure
   2. Adjust other settings as needed...
   3. Make movie