[phenixbb] Issues with refinement of cadmium

[Pavel Afonine]

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?
>

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