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 <[email protected]> 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]> 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 > > >
