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5.  There are plenty of tutorials and how to make a movie with PyMOL.  A simplistic way is to check the "Ray trace frames" and "Cache frame images" in movie menu, hit the play, wait for PyMOL to render all the images (it will eat cpu until it's done) button and the File->Save Movie As->PNG Images.  This will create the numbered sequence of PNG files.
 
5.  There are plenty of tutorials and how to make a movie with PyMOL.  A simplistic way is to check the "Ray trace frames" and "Cache frame images" in movie menu, hit the play, wait for PyMOL to render all the images (it will eat cpu until it's done) button and the File->Save Movie As->PNG Images.  This will create the numbered sequence of PNG files.
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Alternatively, the following command
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grep MODEL morph.pdb | sort -k2 -nr | sed -n 1p | awk '{for(i=1;i<=$2;i++) printf "set state, %d\nray 640,480\npng image%d.png\n",i,i;}' > pngmaker.pml
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will create the pngmaker.pml which is the script file to run from pymol (after you loaded your morph.pdb and chose the presentation you want) to generate the sequence of ray-traced images.
    
6.  Make the movie file with the following command (but of course there are other more GUIsh ways to do this)
 
6.  Make the movie file with the following command (but of course there are other more GUIsh ways to do this)
    
''ffmpeg -qscale 5 -r 20 -b 9600 -i image%04d.png movie.mpg''
 
''ffmpeg -qscale 5 -r 20 -b 9600 -i image%04d.png movie.mpg''
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