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.eduwrote: 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-
Re: [ccp4bb] HKL2000 sigma cutoff
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.eduwrote: 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-
Re: [ccp4bb] HKL2000 sigma cutoff
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
Re: [ccp4bb] HKL2000 sigma cutoff
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
Re: [ccp4bb] HKL2000 sigma cutoff
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.eduwrote: 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
