Hi:<br><br>I am trying to use phenix.elbow to generate restrains for a substrate. I notice that the PDB file produced by elbow contains&nbsp; some&nbsp; broken bonds.&nbsp; So I&nbsp; ran the elbow with the internal strings ATP. The output PDB file also harbors broken bonds. The --opt did help a little. But some bonds still look weird. I am wondering if this a bug or I just didn&#39;t install phenix right. I use the latest version of phenix and default setting.<br>
<br>Thank you very much!!<br><br>Houjin<br>