[phenixbb] Exploded ligands and phenix...

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Apr 28 09:42:18 PDT 2009

Hi Ruben,

> I'm using phenix for the refinement of my protein (phenix.refine). But  
> there is a problem...

Your pdb and cif file seem OK after a quick check (phenix.pdbtools
--geometry-regularization tre.pdb tre.cif).
My best guess is that the ligand conincides with a symmetry operation.
Are the coordinates in the pdb file you posted similar to the coordinates
in the file you used for refinement?
Could you send me the CRYST1 card?
The phenix.refine log would also be helpful.
Note that all geometry restraints are listed in the .geo file written
by phenix.refine. Look for nonbonded interactions involving your ligand.


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