[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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