[phenixbb] Iodide scattering factor

[Pavel Afonine]

  Hi Owen,

to be sure, try both and check the .log file - this will avoid 
guesswork. However, I think "I1-" should work.

Pavel.


On 7/14/10 2:22 PM, Owen Pornillos wrote:
> 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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>>
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