run

   1 mkdir -p saves video
   2 ./clean $1
   3 ./sic $1
   4 if [ "$?" == "0" ]; then
   5         #./perms
   6         if [ "$1" ] ; then
   7                 rasmol -nodisplay < $1/visualize.scr > /dev/null 2>&1
   8                 ./ppm2avi $1
   9         fi
  10 fi