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
