corner in x = 59, y = 31, z = 23, and the "higher" corner in x = 67, y = 39, z = 31 (all values in A). The -c flag specifies the base-name of the generated <code>.cmd</code> files; it has been applied in this example to avoid overwriting the previously generated <code>run_jaws.cmd</code> file.
</p>
<p>
<h5>Running JAWS specifying the number of waters</h5>
When protoms is run such in the initial example (first section in the tutorial), or in the example above, the default is chosen for the amount of water mo