[phenixbb] difficulties with the refinement of a Cadmium containing pdb file

Vellieux Frederic Frederic.Vellieux at ibs.fr
Thu Apr 7 05:53:43 PDT 2011

Hi all,

I have some difficulties refining (what happens is an error status, i.e. 
no refinement taking place) of a coordinate file that contains Cadmium 
ions. The person here who has already refined a structure containing Cd 
ions using Phenix is not here at the moment (otherwise I would have 
asked him). In case you wonder: the CD is shifted 1 position to the left 
as is required for metal ions in a PDB.

Phenix choked. So I ran ReadySet on the input pdb file and gave the 
output file to Phenix for the next attempt. Still failed, and the error 
message I get is:

Fatal problems interpreting PDB file:
Number of atoms with unknown nonbonded energy type symbols: 2
Please edit the PDB file to resolve the problem and/or supply a Cif file 
with matching restraints definitions, along with apply_cif_modification 
and apply_cif_link parameter definitions if necessary.
Also note that phenix_ready_set and phenix.elbow are available for 
creating restraints definitions (CIF files).

Running phenix.elbow (phenix.elbow input_file.pdb --do-all)
does not seem to do anything - no output file seems to be generated. 
Hence I am quite at loss here. Ready Set (from the gui) generated a file 
called name_of_the_coordinate_file.metal.edits , which is used by phenix 
for the next attempt but which does not seem to solve the problem.

Thanks for any advice,


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