Re: [ccp4bb] SAD: Refine against anomalous data

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

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Subject: Re: SAD: Refine against anomalous data
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-08-12

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From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-08-12

Subject: Re: SAD: Refine against anomalous data
From: Paul Adams PDAdams {- at -} LBL {- dot -} GOV
Date: 2007-08-12

Dear George,

you are correct - this kind of refinement only makes sense if F+ and
F- are kept unmerged. The refinement of f'/f'' is performed with the FFT
(from what I recall - Ralf can confirm or deny). At the very least,
structure factors from non-anomalous atoms are calculated using the FFT,
and the anomalous atoms by direct summation. Either way, the inclusion
of anomalous atoms doesn't add any perceptible cost to the refinement.
The multi-wavelength f'/f'' refinement in SHELX sounds very
interesting. We currently cannot do that in phenix.refine (refinement is
limited to one dataset, thus one wavelength). Although it may be
implemented in the future.

Cheers,
Paul

George M. Sheldrick wrote:
> Dear Paul,
>
> That implies that phenix refine (like SHELXL, but unlike REFMAC) can
> refine against data for which I+ and I- (or F+ and F-) have not been
> merged. An attempt to refine f" against Friedel merged data would be
> very poorly determined. Am I right in guessing that phenix refine can
> only do this when then structure factors are calculated by the
> classical summation and not by FFT?
>
> Given relatively high resolution MAD data, it is at least theoretically
> possible using SHELXL (and presumably also phenix refine) to refine
> against I+ and I- for all wavelengths at once, this should give much
> better occupancies for the selenium atoms (in the case of SHELXL it
> would be necessary to use HKLF 2 input format so that a wavelength is
> specified for each reflection, refine batch scale factors, use the
> LAUE instruction so that the program can work out f' and f" for each
> reflection, and - at least when each site is assumed to be Se or S in
> different ratios - use 'free variables' for the Se occupancies). If anyone
> is MAD enough to try this, I would also recommend scaling against a
> reference dataset (e.g. high energy remote) rather than scaling the data
> for different wavelengths separately. There is a suitable option in SCALA
> and SADABS and possibly in other scaling programs as well.
>
> Best wishes, George
>
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-3021 or -3068
> Fax. +49-551-39-2582
>
>
> On Sat, 11 Aug 2007, Paul Adams wrote:
>
>> Hi Ethan,
>>
>> if you want you can specify and refine both f' and f'' for any user selected
>> atoms in phenix.refine:
>>
>> http://www.phenix-online.org/download/
>>
>>
>> Cheers,
>> Paul
>>
>> On Aug 11, 2007, at 9:48 PM, Ethan A Merritt wrote:
>>
>>> On Saturday 11 August 2007 21:41, Miller, Mitchell D. wrote:
>>>> Hi Ethan,
>>>>
>>>>> I have been wanting a way to instruct refmac to accept a user-
>>>>> defined
>>>>> f' term since about forever.
>>>> According to Garib's latest release notes, a command was
>>>> added to refmac 5.3.0015 and later to allow f' to be specified.
>>>> I have not tried it myself yet.. see
>>>> http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html
>>>> "Anomolous form factors
>>>>
>>>> anom formfactor [Name] [f'] [f'']
>>>>
>>>> It will modify form factor of the given atom and use f' part only"
>>>
>>>
>>> Thanks,
>>>
>>> Ethan
>> --
>> Paul Adams
>> Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Laboratory
>> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
>> Head, Berkeley Center for Structural Biology
>> Deputy Principal Investigator, Berkeley Structural Genomics Center
>>
>> Building 64, Room 248
>> Tel: 510-486-4225, Fax: 510-486-5909
>> http://cci.lbl.gov/paul
>>
>> Lawrence Berkeley Laboratory
>> 1 Cyclotron Road
>> BLDG 64R0121
>> Berkeley, CA 94720, USA.
>> --
>>
>>

--
Paul Adams
Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Head, Berkeley Center for Structural Biology
Deputy Principal Investigator, Berkeley Structural Genomics Center

Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909
http://cci.lbl.gov/

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.
--

CCP4bb navigation

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

Previous message:
Subject: Re: SAD: Refine against anomalous data
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-08-12

Next message:
Subject: CCP4 rotation convention
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-08-12