Hi Fred,

Cd ions should create no problem for phenix.refine and you don't need to run any additional program... Make sure it is defined in your PDB file like this:

HETATM 711 ZN    ZN A1400      -1.928 -11.394 -27.827 1.00 17.21          ZN2+
                                                                              ^^
                                                             Put the charge here

Charge is optional, but note: phenix.refine does not infer the charge from the atom name.
It has to appear in the PDB charge columns 79-80 as shown above.
To make sure it is recognized correctly, look in phenix.refine log file - in the above example you would see something like this:

Number of scattering types: 6
    Type Number    sf(0)
     Zn2+     2     28.00
     S       13     16.00
     Na       2     11.00
     O      240      8.00
     N      113      7.00
     C      442      6.00
    sf(0) = scattering factor at diffraction angle 0.

Pavel.

On 4/7/11 5:53 AM, Vellieux Frederic wrote:

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,

Fred.
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