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

Ryan Spencer rspencer at uci.edu
Tue Nov 5 07:46:16 PST 2013

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. 




From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] 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! 


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