On Thu, 2009-10-22 at 10:18 -0400, protein.chemist protein.chemist wrote: > What is the Sigma Cutoff that one should use for Data Processing using > HKL2000. >
Since you say HKL2000, I assume that you mean the "Refinement Sigma Cutoff" in index tab. The parameter, imu, determines which reflections will be considered "strong" and used in parameter refinement and (?) profile fitting. The default value is 5.0, which is just fine for good data. I do, however, routinely set it to lower value of 3.0, since it was my observation that then you get higher redundancy/completeness in lower resolution shells. There is some evidence that the mechanism here is related to rejections due to incomplete profiles. Obviously, as you reach the outer rim, strong reflections become sparse and if you are also using the relatively small default value of the profile fitting radius, large number of reflections may be rejected because denzo can't calculate average profiles in their vicinity (I expected that in the absence of the profile the integrated intensity should be used instead, but perhaps it's not the case). > Is there a minimum or maximum value. > I'd say it makes no sense to go below 1.0, but you can sure try and see what happens. Upper limit is obviously defined by the point where you don't have enough strong reflections for robust refinement of parameters. The absolute values will, of course, vary from dataset to dataset. --
