[phenixbb] Iodide scattering factor

Owen Pornillos owen at scripps.edu
Wed Jul 14 14:22:30 PDT 2010


Thanks!  Just to clarify, should I define the iodide as "I-" or "I1-"  
in the PDB file?

Owen

On Jul 14, 2010, at 5:19 PM, Pavel Afonine wrote:

>  Hi Owen,
>
> no, it's not the case anymore: phenix.refine uses the charge, and this
> is available in phenix build 1.6.1-343 or higher. The charge must be
> defined in PDB file:
>
> Example:
>
> HETATM  711 ZN    ZN A1400      -1.928 -11.394 -27.827  1.00
> 17.21          ZN2+
>
> To be sure it works, in the phenix.refine output, look for:
>
>   Number of scattering types: 6
>     Type  Number    sf(0)
>      Zn2+     2     28.00 <<<<<< HERE
>      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 7/14/10 2:04 PM, Owen Pornillos wrote:
>> Hi BB,
>>
>> I am refining a structure that contains iodide ions.  I remember some
>> previous posts that PHENIX does not take into account the charge  
>> state
>> and uses scattering factors for neutral atoms only.  Is this still  
>> true?
>>
>> Thanks,
>>
>> Owen
>>
>>
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