Well, the output.sca file contains only 64000 lines ( reflections) while the logfile lists ~ 73000 reflections, corresponding to about 100% completeness. So I don't understand why only 64000 are written out. The sigma cutoff was just a guess, but may not be the reason.
Ursula On 7/5/13, Phil Jeffrey <pjeff...@princeton.edu> wrote: > Ursula, > > I/sigI of -3 as I recall. > > Are you sure that the downstream programs you are using aren't the ones > applying the cutoff ? Scalepack is, in general, perfectly happy to > write negative intensities to output.sca and certainly is doing so as of > HKL3000. Perhaps you need to use the TRUNCATE YES option in Truncate ? > Does the output MTZ from Scalepack2mtz show the number of reflections > you expect ? > > > Phil Jeffrey > Princeton > > On 7/5/13 3:24 PM, Ursula Schulze-Gahmen wrote: >> Sorry for the non-CCP4 question. >> >> I am confused about the sigma cutoff used by HKL2000 for scaling. I >> scaled a data set to 3.0 A resolution. I collected a complete dataset >> to 2.8A, but the I/sigma is about 1.0 at 3.0 A. The scaling logfile in >> HKL2000 shows 100% completeness in the highest resolution shell, but >> about 50% of the reflections are below I/sigma =0 in the highest >> resolution shell. I am guessing that these negative reflections are >> not being written out, because the output file from HKL200 does not >> have 100% completeness anymore. I would like to include these negative >> reflections. Is there a setting in HKL2000 that I can change or do I >> need to switch to a different program. >> >> Ursula >> > > -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220
