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 wrote:
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 deviations are
rejected. However,
in the code this seems to be less than minus 3.7 standard deviations (rather
than 4). So
for data that has been processed by TRUNCATE, I think that the observed
criterion sigma(I)
is -3.7. This is hard-wired in the code.
It is interesting (perhaps) that this number only seems to be requested for PDB
depositions processed by RCSB, PDBe do not seem to ask for this (at least, not
the last
time I deposited).
Andrew
Edward Berry:
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 errors of measurement, anything that
comes
in below -3 sigma is likely to be a fluke and should be discarded.
I'm not sure whether this refers to measurements before adding partials, or to
the
summed full reflection observation. anyway, I always put -3s for that value
and haven't had any negative feedback from the annotators.
Matthew Franklin:
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 (i.e. use all F's) for this one.
I have no idea what Scala does.
On 25 Nov 2013, at 09:21, Graeme Winter <[email protected]
<mailto:[email protected]>> wrote:
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 coming up with
/Data processing information/: high and low resolution limits, observed
criterion sigma
(F) cut-off or observed criterion sigma (I) cut-off, number of unique measured
reflections (all and observed), percent of possible reflections observed,
R-merge I
(observed) or R-sym I (observed), details about the highest resolution shell
Can anyone point me in the right direction?
Thanks in advance & best wishes, Graeme
