Can anyone explain what Zbyszek Otwinowski means by Chi squared? I can't find a
definition in any of his papers (though I may have missed it). Is there a
reference?
It doesn't seem obviously related to the chi squared distribution ("In
probability theory and statistics, the chi-square distribution (also
chi-squared orχ²-distribution) with k degrees of freedom is the distribution of
a sum of the squares of k independent standard normal random variables. "
http://en.wikipedia.org/wiki/Chi-square_distribution)
Phil
On 29 Jun 2010, at 21:14, Felix Frolow wrote:
> Graphical information from Scalepack as used in HKL2000 is of unprecedented
> help to detect anomalous signal. Anomalous detection for S anomalous data
> using
> CHI**2 and Rfactor statistics for reflections with averaged and separated
> Bijvoet pairs is attached. It is very well described in HKL2000 manual. There
> is nothing special about data collection
> (strategy was used) and measurement was relatively fast (4 h on MicroMax007
> and RaxisIV++).
> BTW Rfactor is 1.9% with separated Bijvoet reflections and 2.6% with averaged
>
>
> BTW James Holton website calculate for this case 0.078 crystal
>
> Dr Felix Frolow
> Professor of Structural Biology and Biotechnology
> Department of Molecular Microbiology
> and Biotechnology
> Tel Aviv University 69978, Israel
>
> Acta Crystallographica D, co-editor
>
> e-mail: [email protected]
> Tel: ++972-3640-8723
> Fax: ++972-3640-9407
> Cellular: 0547 459 608
>
>
>
>
>
>
>
>
> Quoting "Bernhard Rupp" <[email protected]>:
>
>> I second the hkl2map/SHELXCDE approach. Two complete examples
>> explaining how to do this for MAD and S-SAD cases are in my book.
>> I wish to emphasize the importance of
>> a) running enough trials
>> b) careful selection of resolution cutoffs
>> c) look at the solution distribution
>> d) play with SHELXE parameters.
>> The hkl2map graphs are enormously helpful for this purpose.
>>
>> BR
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Tim
>> Gruene
>> Sent: Tuesday, June 29, 2010 2:29 AM
>> To: [email protected]
>> Subject: Re: [ccp4bb] measure of anamolous signal
>>
>> Dear Murugan,
>>
>> you can use the program hkl2map from Thomas Schneider, available at
>> http://webapps.embl-hamburg.de/hkl2map/
>> It's a graphical interface to the programs shelx c/d/e which are available
>> from http://shelx.uni-ac.gwdg.de/SHELX/index.html
>>
>> With SAD data you want to look at the d"/sigma line at the end of the shelxc
>> output. Where that drops below about 1.3 is approximately where your
>> anomalous signal ends. You might get slightly improved statistics with xprep
>> instead of shelxc, but xprep is not free and you have to get a copy from
>> Bruker-AXS.
>>
>> Tim
>>
>> On Tue, Jun 29, 2010 at 02:35:29PM +0530, Vandu Murugan wrote:
>>> Dear all,
>>> I have collected a 2.7 angstrom home source data with Cu-Kalpha
>>> source for a protein with 6 cysteines, with a multiplicity of around
>>> 23. I need to know, is there any significant anamolous signal present
>>> in the data set, since there is no good model for my protein. Can any
>>> one tell, which program to run, and what parameter to see? Thanks in
>> advance.
>>>
>>> cheers,
>>> Murugan
>>
>> --
>> --
>> Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>>
>
>
>
> Dr Felix Frolow
> Professor of Structural Biology and Biotechnology
> Department of Molecular Microbiology
> and Biotechnology
> Tel Aviv University 69978, Israel
>
> Acta Crystallographica D, co-editor
>
> e-mail: [email protected]
> Tel: ++972-(0)-3640-8723
> Cel: ++972-0547-459-608
> Fax: ++972-(0)-3640-9407<detectionOfAnomalousSignalBy Scalepack-HKL2000.pdf>
