h the graphical representation options in VMD):
</p>
<img src="density.png"  alt="" />
<p>
A different visualization option are the clusters. These can be generated going to your out folder and using the following command</p>
<pre>
python $PROTOMSHOME/tools/calc_clusters.py -i all.pdb -m WA1 -a O00
</pre>
and then visualized with
<pre>
vmd -m clusters.pdb ../protein.pdb ../fragment.pdb
</pre>
<p>
You should be looking at something similar to the image below, after tweaking the graphical representation optio