How does PHENIX know where to look for proper bond lengths and angles for a metal ion I add to a protein structure - do I just add the metal into difference density and any waters, and then run ready set and it knows where to look for that particular metal and the atoms to which is is coordinated?  And shouldn&#39;t there be a &#39;cif file that it outputs, or is that something that I need to get myself?  Sorry it&#39;s still not obvious to me from the documentation.<br>
<br>Thanks<br><br>Laurie Betts<br>