Hi Mohammad,

could you please describe steps you have done and at what point this happens? Apart from water (optionally), phenix.refine would not add or remove atoms.

Pavel

I am trying to fit Cd ion in a protein structure using Phenix. However, the refinement transposes CD to DC and returns me a result with DC (2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE) in the validation report and gives me the missing atoms accordingly. When I open the same structure in Coot, it shows me the ion Cd. Also, the .pdb file contains Cd.

 

Cd is present in my crystallization condition and fits well into the density. Other metal atoms such as Zn and Cl have refined well.


HETATM 5535 CD    CD F   1     156.533 -64.594 138.360  1.00 76.11          CD
HETATM 5536 CD    CD F   2     119.954-111.545 105.562  1.00 35.85          CD
HETATM 5537 CD    CD F   3     152.936 -93.077 102.747  1.00 28.68          CD
HETATM 5538 CD    CD F   4     121.467 -96.375 128.574  1.00 72.24          CD

 

Can someone suggest what may be wrong?