Creating animation movies from Appended Scenes in Pymol

Freemol Installation:

To be able to save movie mpg files from within pymol first install the Freemol utilities using subversion. If you dont have subversion you can install it on ubuntu ( sudo apt-get install subversion). Then run the comman below

 svn co svn://bioinformatics.org/svnroot/freemol/trunk freemol-trunk

Set your FREEMOL environment variable in csh or bash to the directory where you have the bin,include,lib ..etc directories after you pull the subversion repository. In my case

harijay@xtalmachine:~/freemol-trunk/freemol$ ls
bin  include  lib  libpy  licenses  LICENSE.txt  README.txt  share
 

for eg in bash

export FREEMOL=/home/harijay/freemol-trunk/freemol

Then you will cd into the src ( source) directory

Which in my case is in /home/harijay/freemol-trunk

cd /home/harijay/freemol-trunk/src

Here you will see the freemol components. Individually cd into each directory . Make sure your FREEMOL environment variable is setup and then run 

./configure

make

make install

This shoould install the freemol components to the $FREEMOL/bin/ directory

So in my case

harijay@xtalmachine:~/freemol-trunk$ ls $FREEMOL/bin/

apbs  apbs.exe  mengine.exe  mpeg_encode.exe

Now put the $FREEMOL/bin directory into your path in your ~/.bashrc or other file. Make sure the bin directory is in your path

export PATH="$PATH:$FREEMOL/bin"

Making a movie from appended scenes in Pymol

From Pymol build 1.2 onwards , pymol allows you to build movies directly from scenes defined using the "Scene-Append menu item". To do this you will create the scenes combining the views and representations you want and then use the command the command "Movie" - Program - Scene loop - Y rock , then pick a time for which the given scene should rock between camera interpolations .

This assumes that you have freemolconfigured and available on your path. Failing which you can always save the images and make the movie externally. This very convenient functionality makes movie making a pretty WYSIWYG process.

To quote Warren from a recent pymol newsgroup post

Assuming that you are using the most recent PyMOL 1.2 beta build, first create a Scene for each display you wish to show.

(To do that, show everything the way you want and then select “Append” from the “Scene” menu. Repeat the process for each view / color / representation you wish to show. You can PgUp / PgDown through defined Scenes.)

Then, to create the movie, select “Program -> Scene Loop -> Y-Rock -> # seconds each” from the “Movie” menu.

Now you can write out the movie as either a series of PNG files or an MPEG file using “Save Movie As…” from the “File” menu. Using scenes to create movies is a lot easier than messing around with scripts : )! Cheers, Warren