HI Wei, The pdb of the ligand probably had an occupancy of 0.00 when you brought it into Coot. The easiest way to handle it is to just change all the occupancies of the ligand back to 1.00 in the pdb. If the ligand has partial occupancy then phenix might be dropping it down to 0.00 if you have the 'refine occupancies' box checked. I've seen this before when doing MR with ligands that phenix does not recognize without the corresponding .cif. Ryan From: [email protected] [mailto:[email protected]] On Behalf Of Wei Shi Sent: Tuesday, November 05, 2013 6:45 AM To: PHENIX user mailing list Subject: [phenixbb] Green density for ligands in places where the ligand is in density Hi guys, I am working with a protein-ligand complex structure. I generated the ligand pdb and cif with Phenix.eLBOW. Then, I fit the ligand to density (green or continuous blue denisty) in Coot. Then, I did a refinement of the protein-ligand complex model in Phenix. I opened the refinement results in Coot, I don't know why in some places where the ligand is in density, it always shows green density in Coot... And, from the pdb file, the occupancy for all ligands are 0? Do any of you happens to know whether this is unusual and what might go wrong? Thank you so much! Best, Wei