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

[Bart Hazes <bhazes@ualberta.ca>]

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On Tue, 18 Sep 2001, 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?

No you didn't do anything wrong. The 89.3% with the zero sigma cutoff is based
on all positive intensity reflections. With the -three sigma cutoff you are
getting also the reflections that were measured with a slight negative
intensity giving you 97.8%. Truncate will create weakly positive amplitudes
from these negative intensities by "truncating" the probability distribution,
e.g. only considering the tail of the distribution that corresponds to a
positive intensity. Read the paper for details.

Are you sure that CNS is applying a  F/sigma(F)>2 rejection criterium. If so
is it just for statistics or is it not using those reflections for refinement.
I guess it will be the former.

Bart

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