Dear All,<div><br></div><div>I am refinining a protein-NAD complex structure at ~1.9A resolution.</div><div>I have included a main conformation for my NAD ligand but while I see clearly the position for the nicotinamide- first ribose part, my density bifurcates when it comes to the second ribose-adenine. It seems that I have two (at least) conformations for this part of the ligand molecule.</div>

<div><br></div><div>Can I refine these two alternate conformations in Phenix knowing that a part of the ligand will be common (have an occupancy of one) while the two other ones will be separate?</div><div><br></div><div>

Do I need to enter two ligand molecules or do I have to do more elaborate things?</div><div><br></div><div>Last question is it possible that for the variable regions I may end up with a sum of occupancies that is not 1 while for the fixed region it might end up being one?</div>
<div><br></div><div>That&#39;s three questions for the wizards.</div><div><br></div><div>Thanks in advance.</div><div><br></div><div>Pascal Egea</div><div>UCSF</div>