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

Vellieux Frederic Frederic.Vellieux at ibs.fr
Fri Apr 8 00:19:44 PDT 2011


Hi Pavel,

Indeed there was no charge on the Cd ions, and some of these Cd ions had 
improper annotations in columns 77-78. I must admit that I do not 
understand why these columns are used while the data (atom type) is 
provided before on the HETATM (or ATOM) record.

Refining now (I hope).

Fred.

Pavel Afonine wrote:
> 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.


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