Re: [ccp4bb]: Question about I to F conversion

["Aleks Roszak" <aleks@chem.gla.ac.uk>]

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Hi Jeff,

When you are using zero sigma cutoff in Scalepack, you are cutting off negative
I's, and that gives you lower completeness of your data. When using -3 sigma
cutoff, you keep most of the negative I's, and then program TRUNCATE (with
'TRUNCATE YES') can use them to estimate F's for those obviously very weak
reflctions. As a result these reflections are not excluded and the completeness
is higher.

Aleks

On Sept 18, Jeff Taylor wrote:
>
> I need some help understanding what I'm seeing in my data completeness
> before and after conversion from intensities to amplitudes.
>
> My data set is from a crystal with a large unit cell and therefore has a
> large number of reflections.  I have processed the data with denzo and
> scalepack.  To get an idea of the data quality and completeness I looked
> at the statistics from a scalepack run using a zero sigma cutoff and
> found an overall completeness of 89.3% (see table below).  I then ran
> scalepack again using a -3 sigma cut and converted the resulting
> reflection file to amplitudes using the CCP4 program Truncate, with
> Wilson scaling.  Now when I look at the completeness of the resulting
> reflection file in CNS I get an overall completeness of 97.8% (see table
> below).
>
> How can it be that there are more reflections with F/sigma(F)>2 than
> there were with I/sigma(I)>0 ?
>
> Does Wilson scaling or any other correction applied to the data by
> Truncate change the I/sigma(I) ratio for a particular reflection?  Did I
> do something wrong in the conversion process?
>
> Thanks for any help,
>
> Jeff Taylor

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* Aleksander W. Roszak, Ph.D.               E-mail: aleks@chem.gla.ac.uk *
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