Making movies in PyMol using Adobe ImageReady:
Here is how to make a simple movie using pymol and Adobe ImageReady, which comes with PhotoShop 7. I am using one coordinate file and have set pymol to rock the molecule back and forth, but any other pdb file and script obviously will work fine too.
1. Download this sample coordinate file called low.pdb (save it as an ascii text file).
2. Download this sample pymol script called low.pml (save it as an ascii text file). You can use it as an example for making your own movies.
3. Make a directory, put both of these files into it, and then cd to that directory and issue the command after the user prompt %:
% pymol low.pml
The molecule will display as a full screen image.
4. Now to start the movie-making process, type the following command in the display window after the PyMOL > prompt:
PyMOL > set ray_trace_frames = 1
PyMOL > mpng prefix
(The word prefix should be substituted with whatever prefix you want to use for all of the images, i.e, prefix_0001.png is the first image.)
5. Get a cup of coffee.
In this example it will crank out 60 ray-traced png images. It takes a few minutes.
6. Open up Adobe ImageReady 7.0 (comes with Adobe Photoshop 7.0).
7. Go to the "File" pull-down menu and choose "Import > Folder as Frames" and choose the directory you made in step 3. It will now import all of the png images and you will see them displayed as little icons in the "Animation" menu. You can now test your movie with the little buttons that appear below it, set the time for each frame, etc.
8. Now you can save the movie:
To make a QuickTime movie, use "Export Original" under the "File" pull-down, and choose QuickTime movie.
To make an animated gif, use "Save Optimized As" with "Images Only" and it will make an animated gif for you.
9. Here is Apple's directions for how to embed a Quicktime movie into a web page so that even Micro$oft Internet Exploder will display it. Animated gifs just get embedded as if they were still images. Here is an example of both, side by side.
