I found a fix, but not an explanation. I scaled the same data with scalepack and had no problem with loosing reflections. I am not sure what happened in HKL2000.
Ursula On Fri, Jul 5, 2013 at 12:38 PM, Phil Jeffrey <[email protected]>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
