> > > Chi2 is unusually high at lower resolution (Chi2 is >3 from 3.5A as > shown > > > below) and there is a relatively high percentage of rejections (>1.5 %). > > > > > > > Chi^2 in Scalepack *must* be adjusted by changing the expected errors to be > about 1. > Until then, I would not reject reflections. Only then I would reject > reflections and then readjust chi^2 to be 1 again. > Having said that its quite a while since I used scalepack. > Maybe in the age of automation scalepack does this now automagically in the > context of HKL2000, but a Chi^2 of 3 > at low resolution indicates that some reflections and very likely their > sigmas do not have realistic intensities, and also > that your rejections might be excessive.
Just a point here. The high chi^2 values you see in the scalepack output are because of the *anomalous signal*, not because of any pathology with the data. I assume scalepack was run with the 'anomalous' card specified. In this case (I believe) the + and - reflections will be treated as equivalent for scaling and calculating statistics, but will be written to the .sca file separately. Chi^2 will be screwed up because it detects a large deviation from random in the reflections (i.e. the anomalous difference between I(+) and I(-). You might actually be rejecting the reflections with the *most* anomalous signal since they are the ones that deviate furthest from your random-noise model. If you want your chi^2 values to be meaningful you need to use the 'scale anomalous' card to separate I(+) and I(-) for scaling/statistics as well as the output .sca. The scalepack manual warns against this flag, but I've never had a problem using it (so long as you have reasonably redundant data). So, re-process with 'scale anomalous' and then run autoSHARP in all sub-spacegroups of P212121 - as Tassos will tell you this works a treat! Cheers, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
