I wonder if the "rejects" file had a large number of reflections in it in one case, but not in the other case. One can be playing with various options and create or add to such a large list. That's why there is the "Delete Reject file" option.
Jim ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Sunday, July 07, 2013 11:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] HKL2000 sigma cutoff -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Ursula, in your first email you wrote that you were confused by [...] HKL2000 for scaling, and in this email you wrote that your fix is to scale the data with scalepack. In my understanding scalepack is part of HKL2000 - - would you mind explaining what the difference is to you? Just to understand what caused a problem and how you fixed it. Regards, Tim On 07/05/2013 11:18 PM, Ursula Schulze-Gahmen wrote: > 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 > <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 >>> >>> >> > > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFR2ZqvUxlJ7aRr7hoRAvNoAKDhHx+kbYYAzcTFaF+ywPhu8YMgFQCeJ2Bw NMRDZu6kJdbvKQLJJV4Pe70= =YLIm -----END PGP SIGNATURE-----
