Thank you guys for the suggestions. I changed the occupancy of the ligand to 1 in pdb and do refinement with 'refine occupancies' box checked. The R values dropped about 3-4% compared with before and the occupancy for the ligand stays as 1. Thank you!
Best, Wei On Tue, Nov 5, 2013 at 11:23 AM, Eleanor Dodson <[email protected]>wrote: > It sounds very wrong! But no idea how you fix it.. Edit the coordinate > file and change all occupancies to 1.0? > Or reset occupancies in coot - Look under > Measures > Residue info > Edit occupancy and B > > Eleanor > > On 5 November 2013 14:43, Wei Shi <[email protected]> wrote: > > 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 >
