I tried to model two ligands one of which has two conformations. In other words, the two scenarios are: 1) ligand X with conformation A (XA, 75% occupancy); 2) ligand X with conformation B (XB, 25% occupancy) plus another ligand Y. However, the problem is ligand Y will have steric clash with ligand XA. If I rename ligand X and Y to the same residue name then I do not know how to define the CIF file. 

  I apologize if this question was asked before and I do not know how Phenix or other refinement can deal with multiple conformation a group of ligands. 

Thanks.

Happy new year!

Yang Hai

Christianson Lab

University of Pennsylvania