e>solvate.py</code> script adds the crystallographic waters from the scoop to the droplet. Therefore, we need to remove them from the scoop PDB-file, to avoid duplicates.<p> 
<pre>sed -i -e "/T4P/d" -e "/TER/d" protein_scoop.pdb</pre>
<p>
<li>Next we need to create the set of waters that will form our JAWS waters. This can be done by typing:
<pre>python $PROTOMSHOME/tools/distribute_waters.py -b 59 31 23 8 8 8 -m 10 -o jaws1_wat.pdb </pre>
<p>
with this command, the file <code>jaws1_water.pdb</code> will be