Dear all
I request you please tell me what is the value of Observed criterion sigma
(F) and Observed criterion sigma (I) for any data processed by imosflm and
scala ?
--
Regards
Faisal
School of Life Sciences
JNU
Hi Folks,
A xia2 user wrote in asking where to find
'observed criterion sigma(F)' and 'observed criterion sigma(I)'
in the xia2 logs (i.e. from Scala or Aimless or XSCALE)... I have no idea
what they are so will struggle to give a helpful answer ;o) and
surprisingly google was not a lot of use
Hi Graeme,
There was a CCP4BB thread about this quite recently (14th Nov 2013). I've coped
below responses from Edward Berry and Matthew Franklin.
SCALA AIMLESS have no sigma cutoffs, but TRUNCATE does. According to the
documentation, reflections with intensities less than minus 4 standard
Thanks Andrew, slight feeling of embarrassment now that this was a thread
two weeks ago (though this was off the bottom of the ccp4bb folder and did
not 'google' in my defense... I guess I was also looking in the wrong
place...)
Best wishes, Graeme
On 25 November 2013 11:15, Andrew Leslie
I would note that the cutoff in HKL must be a somewhat different statistic than
that
in truncate, since the former is applied to individual measurements
(observations?)
before averaging, while truncate normally never sees the individual measurements
but only the averages.
Ed
Andrew Leslie
It used to be common to only include reflections for which I x sigma(I) in
refinement, with x often being 3.
However, nowadays this is not considered good practise, as reflections with
small Is are likely to have I 3 sigma(I), but are also important for
refinement.
In small molecule
Always deprecated, hopefully never common!
On 14 Nov 2013, at 11:27, Mark J van Raaij mjvanra...@cnb.csic.es wrote:
It used to be common to only include reflections for which I x sigma(I) in
refinement, with x often being 3.
However, nowadays this is not considered good practise, as
I think it used to be default in denzo/scalepack. Or perhaps it was used to
calculate statistics, but not to exclude reflections...I do remember having to
switch it off.
On 14 Nov 2013, at 12:29, Phil Evans wrote:
Always deprecated, hopefully never common!
On 14 Nov 2013, at 11:27,
As I understand it this refers to the decision whether an observation is valid or not, and
the default value in HKL suite is -3 sigma (note the negative sign). The
denzo/scalepack manual explains that while it is important not to exclude
observations
that are slightly negative due to random
Dear Faisal -
HKL2000 (Denzo/Scalepack) use I greater than -3 sigma (that's NEGATIVE
3) as the observed criterion, so that's what you would put down for this
entry. There is another place where you're asked to provide an observed
criterion for F's used during refinement. I always put down 0
To add one more nugget, in your pdb you might see a
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.36
or some such thing. Ignore it (I am not sure why this isn't closer to
zero, but that must be a result of French/Wilson). This is *not* your
observed criterion for sigma for F's, although
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