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 <[log in to unmask]
> <mailto:[log in to unmask]>> 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
>
|