[phenixbb] Green density for ligands in places where the ligand is in density

Wei Shi wei.shi118 at gmail.com
Tue Nov 5 06:45:06 PST 2013

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!

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