Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Refmac 5.4.0066 versus Refmac 5.4.0034
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-01-02

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Subject: Re: Refmac 5.4.0066 versus Refmac 5.4.0034
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-02

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
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Refmac 5.4.0066 versus Refmac 5.4.0034
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-01-02

Next message:
Subject: Webcast of the CCP4 study weekend ?
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-01-02