Dear all,

I am using the PHENIX version 1.8.1-1168 and need to get the pdb file and the cif file for the metal-chelate complex Gd-DTPA for refinement of a structure. I got the pdb file and the cif file for a dimer of the complex. Then I edited those to contain only one metal chelator complex and used as inputs in elbow. I have attached the pdb file and the cif file I used as inputs.

I gave cif file as chemical file type with pdb file as initial geometry and ran elbow. Then I used pdb file only or cif file only as inputs separately. Every time it ended with the error “Failed to determine the bonding of a fragment of the molecule”

Also I tried using smile string C(CN(CC(=O)[O-])CC(=O)[O-])N(CCN(CC(=O)[O-])CC(=O)[O-])CC(=O)[O-].[Gd+3]and pdb file as inputs. Then it runs without an error, but it outputs cif and pdb files containing only Gd. 

How can I get the cif file for the metal-chelate complex?  I want to use the metal-chelate complex as one entity in the refinement, so that it will have the correct geometry of the chelator. 

 Thanks

Subhani