[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
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
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