[phenixbb] Iodide scattering factor

Owen Pornillos owen at scripps.edu
Tue Jul 20 14:24:42 PDT 2010


Hi -

I've noticed a bug.

It seems that phenix.refine at some point changes the charge state of  
iodide, and outputs the following to the PDB.

HETATM 7801 I      I F   1      18.611  -6.385   1.709  0.66  
54.88           I+1

The same atom in the input file was:

HETATM 7937 I      I F   1      18.600  -6.380   1.702  0.64  
52.59           I-1

Refinement appeared to occur normally, and correct scattering factors  
were declared in the log file:

  Number of scattering types: 5
    Type Number    sf(0)
     I1-     7     53.91
     S      65     16.00
     O    1503      8.00
     N    1372      7.00
     C    5005      6.00

Owen


________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org 
] On Behalf Of Pavel Afonine [pafonine at lbl.gov]
Sent: Wednesday, July 14, 2010 2:25 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Iodide scattering factor

  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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>>> phenixbb at phenix-online.org
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>>
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