MovieSchool 6

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Exporting your Movie

This wiki already has lots of information on how to convert your PyMOL movie to another format. Check out those pages.

Once you've setup your movie as in any of the previous examples, you have a couple options for making a movie.

Export from PyMOL: Newer PyMOLs support

  • File→Save Movie As→MPEG
  • File→Save Movie As→PNG Images

from the menu.

mpeg: This needs a bit of work. The following instructions work with trunk (1.2r2pre). Compile pymol trunk.

Checkout freemol source from

svn co svn:// freemol-trunk

This creates a directory called freemol-trunk. Inside freemol-trunk is a directory called freemol. Now you need to setenv (or export) a variable called FREEMOL pointing to the above folder - freemol). In TCSH and related C-shells:

setenv FREEMOL /my/long/path/to/freemol-trunk/freemol
cd freemol-trunk/src/mpeg_encode

or in bash:

export FREEMOL=/my/long/path/to/freemol-trunk/freemol
cd freemol-trunk/src/mpeg_encode

And then

cd freemol-trunk/src/mpeg_encode

(Ignore all other directories inside directory src. These were unnecessary, at least for me.)

make install

Add these two lines

export FREEMOL

to your pymol script (i.e. /sw/bin/pymol). Launch pymol and Save Movie as MPEG should work now. No need of any complicated codecs.

mpng: You can still use the good old mpng option to save all your frames to disk. You can then compile them into a MPEG (see below).

Old Style: One of the older scripting styles was to make minor changes and dump PNGs. This is essentially obviated with PyMOL's new movie-making functionality. The old style was to simply call cmd.png every time you made a scene change.


  • Movie not ray traced? Make sure you set ray_trace_frames to 1.


See Software_Codecs for information on how to stitch together movies from PNGs and optimize them for great crisp-looking movies.

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