[phenixbb] Exploded ligands and phenix...

Ruben Van der Meeren ruben.vandermeeren at ugent.be
Tue Apr 28 11:56:51 PDT 2009

Hi Ralf,

The coordinates of the ligand in the file I use for refinement are  
similar to those I posted. I uploaded an overlay of the original  
ligand and the ligand in my model. Green is model, blue is original...  
You can see the picture on this site:


The cryst1 card of the pdb is the next:
CRYST1   98.500  104.050  415.200  90.00  90.00  90.00 P 21 21 21

The structure has 4 monomers in which I modeled a ligand monomer A and  
B. I also checked the .geo file. In most cases (for bonds and Angles)  
the model is almost equal to the ideal. For dihedrals there is much  
more disagreement. E.g. for one dihedral the model is 168° whereas the  
ideal is -60°. For non-bound interactions the distance is sometimes  
less than the VDW-radius. Could this be the problem? But this is in  
fact the thing I want to refine.

The log file can be downloaded here:


Citeren "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>:

> 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.
> Ralf
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