As you say - it is 17.006 in all versions of atomsf.lib I have access to!
It is good that f' and f" will now reflect the wave length, although the
wavelengh is so often wrongly recorded that this had better be an
optional request rather than the default!
Eleanor
Ethan Merritt wrote:
> On Thursday 03 January 2008 01:25, Boaz Shaanan wrote:
>
>> Is the wrong value pointed out by Ethan the reason why we tend
>> to nearly always see +ve difference peaks over Se-met after refinement ?
>>
>
> Could be.
> I have attached a plot of the net scattering factor for the two
> sets of values.
>
> I am curious as to exactly which version[s] of atomsf had the wrong
> value for A1. The various old copies I have lying around on my disks
> all contain the correct value.
>
> Ethan
>
>
>
>
>
>> Just curious.
>>
>> Regards,
>>
>> Boaz
>>
>> ----- Original Message -----
>> From: Garib Murshudov <[log in to unmask]>
>> Date: Wednesday, January 2, 2008 19:19
>> Subject: Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034
>> To: [log in to unmask]
>>
>>
>>> On 2 Jan 2008, at 17:15, Ethan Merritt wrote:
>>>
>>>
>>>> On Tuesday 01 January 2008 06:40, Mark A Saper wrote:
>>>>
>>>>> Well, I guess one shouldn't change versions of refmac in the middle
>>>>> of a structure refinement. What are the major
>>>>>
>>> differences between .
>>>
>>>>> 0034 and .0066 ? I noted that form factors for the Se
>>>>>
>>> atom have
>>>
>>>>> changed dramatically even though I'm using the same " anom
>>>>>
>>> formfactor>> SE -8.13 5.05 " command. Is this because the
>>> program is now using
>>>
>>>>> the wavelength on the .MTZ file ?
>>>>>
>>>>> with .0034:
>>>>>
>>>>> SE 8.8706
>>>>>
>>> 2.4098 5.8196 0.2726
>>> 3.9731 15.2372
>>>
>>>>> 4.3543 43.8163 2.8409
>>>>>
>>>> The first coefficient here is wrong.
>>>>
>>>>
>>>>> with .0066:
>>>>>
>>>>> SE 17.0006
>>>>>
>>> 2.4098 5.8196 0.2726
>>> 3.9731 15.2372
>>>
>>>>> 4.3543 43.8163 -11.7969
>>>>>
>>>> These are the values given for a1, b1, ... a4, b4 in Table 6.1.1.4
>>>> of International Tables for Crystallography Volume C (1995).
>>>>
>>>> The value of c (-11.7969) corresponds to an f' value of
>>>> -14.6378 (= -11.7969 - 2.8409)
>>>>
>>>> This could only be possible at the inflection point of the Se
>>>> anomalous scattering curve, and only for a beam with a very narrow
>>>> bandwidth. Current generation beamlines more
>>>>
>>> typically yield an
>>>
>>>> effective f' of -5e to -10e in practice.
>>>>
>>> We have corrected it. It was due to double addition of f' (one
>>> from
>>> anom formfactor and one from a la crossec calculation). Now it
>>> should
>>> not happen
>>>
>>> Garib
>>>
>>>
>>>
>>>> --
>>>> Ethan A
>>>>
>>> Merritt Courier Deliveries: 1959 NE Pacific
>>>
>>>> Dept of Biochemistry
>>>> Health Sciences Building
>>>> University of Washington - Seattle WA 98195-7742
>>>>
>>>>
>> Boaz Shaanan, Ph.D.
>> Dept. of Life Sciences
>> Ben-Gurion University of the Negev
>> Beer-Sheva 84105
>> Israel
>> Phone: 972-8-647-2220 ; Fax: 646-1710
>> Skype: boaz.shaanan?
>>
>>
>
>
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