Changes

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

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

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.  

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 640x480 pixel 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''