ffmpeg \                                                   
    -framerate 90 -i vmd/final.molecule.%05d.tga \                                  
    -framerate 90 -i plot/frame%05d.png \                                       
    -c:v libx264 \                                                              
    -preset slow \                                                              
    -crf 18 \                                                                   
    -filter_complex "\                                                          
        [1:v] scale=in_w*0.8:in_h*0.8 [sclvrl] ;\                               
        [0:v][sclvrl] overlay=eval='init':x=W-w-5:y=5 [overout] ;\              
        [overout] scale=trunc(in_w/2)*2:trunc(in_h/2)*2" \                      
    movie.overlay.mkv                                                             

# syntax for ffmpeg "filters" is
# [in_stream_name] command=parameter1=value1:parameter2=value2 [out_stream_name] ;
#
# The above takes video stream 1 [1:v] and scales it by 0.8
# It then overlays the output of that [sclvr1] onto the vmd movie [0:v]
# The final line rounds the whole video to have a width and height divisible
# by 2, which is something needed by h264 (??). I think the default width for
# vmd is an odd number.