[phenixbb] Issues with refinement of cadmium
Pavel Afonine
pafonine at lbl.gov
Mon Feb 26 17:20:43 PST 2018
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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