ffmpeg -i molecule.%5d.ppm -c:v libx264 -preset slow -crf 18 molecule.mkv

# -i       input filenames
# -c:v     codec (libx264 --> H.264)
# -preset  duh
# -crf     quality factor, lower = better, 18 = practically lossless
#          output filename

# For colors, make sure you're using yuv444 which should be the default in newer ffmpeg

# Note: you can use either the vmd ppm or tga image files