Because of the differences between Molscript and Bobscript, I have written a script to transform my molscript commands to something that will (usually) work in Bobscript. Of course, you have to stick the Bobscript commands in once and then comment them out, but this can really speed up the tweeking time of an image by letting you use molscripts opengl mode while editing the file.

I call this tobob

     #!/bin/sh
     #Use tobob [molscript file]
     #
     if [ $1 ]; then input=$1
      else echo "Please pick a Molscript input file.  These \".ms\" files are available:"
      echo ; ls *.ms ; echo ; echo -n "Which one?  " ;read input
     fi
     root=`echo $input |awk -F . '{print ($1)}'`
     echo
     
     sed -e 's/background/!background'/ \
         -e 's/!map/map/' \
         -e 's/transform atom \*/transform all/' \
         -e 's/!set maplinewidth/set maplinewidth/' \
         -e 's/!set mapcolour/set mapcolour/' \
         -e 's/!set coverradius/set coverradius/' \
         -e 's/!contour mymap/contour mymap/' \
         -e 's/set colourparts on;/set sticksegments 2;/' \
         -e 's/set colourparts off;/!set colourparts off;/' \
         -e 's/!colour ball-and-stick/colour ball-and-stick/' \
         -f /usr/ginsberg1/dcoop/Molscript/colorsubs.sed \
       $root.ms >$root.bs
     

Here is the file colorsubs.sed. It allows you to use the Molscript color descriptions without having to manually change to the RGB equivalent.