Re: [ccp4bb] Rmerge of the last shell is zero
Great! and (oops) now I realize what I meant to say was compare cc* with cc-work and cc-free. eab Nat Echols wrote: On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry ber...@upstate.edu mailto:ber...@upstate.edu wrote: If you refine once in phenix you can use phenix.cc_star to calculate cc* and compare with R and R-free; from the output mtz file and your unmerged .sca file. FYI, this should also work with structures refined in Refmac, assuming it can recalculate the R-factors to within a reasonable margin of error. -Nat
Re: [ccp4bb] Rmerge of the last shell is zero
lies in the fact that you used HKL2000. Scalepack has a long standing feature where it reports Rmerge 100% as zero. Quite why they do that is a mystery, but your Rmerge in the outermost shell is NOT zero - the Rmerge for the lower resolution shells will show up as non-zero if Rmerge 100%. That feature is overdue for a fix. Alternatively export your scaled data with NO MERGE ORIGINAL INDEX and import into CCP4 via Pointless and have Scala or Aimless report the correct statistics. Reprocessing the data using XDS or Mosflm will ultimately lead you to scaling the data with a program that doesn't have that bug. If you do this, report Rmeas rather than Rmerge, the former being a better measure. Phil Jeffrey Princeton *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen [yafangche...@gmail.com] *Sent:* Wednesday, August 14, 2013 11:32 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Rmerge of the last shell is zero Dear All, Here are some more details about the question I asked earlier about Rmerge is 0 in the last shell. I processed the data using HKL2000. The space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back the resolution any more. But I don't know how to explain Rmerge in the last shell being 0. Besides, I am wondering if this data is publishable (with Rmerge being 0 in the last shell). Thank you so much for your help! Best, Yafang On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.com mailto:yafangche...@gmail.com wrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907
Re: [ccp4bb] Rmerge of the last shell is zero
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Yafang, a mathematically simple answer would be you collected no symmetry equivalent reflections, although experimentally this is probably difficult to achieve, unless your space group is P1. If you could tell the name of the software you used, the respective developers might know if '0' indicates something specific. Regards, Tim On 08/14/2013 04:59 PM, Yafang Chen wrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSC6C5UxlJ7aRr7hoRAvgiAJ9uGurdV1F1NbwMShnGBQforDPnGgCg7IZ7 6lz3MWS/qAsmAsX6Wf8f4Tg= =l/px -END PGP SIGNATURE-
Re: [ccp4bb] Rmerge of the last shell is zero
multiplicity = 1.0? On 14 Aug 2013, at 15:59, Yafang Chen yafangche...@gmail.com wrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907
Re: [ccp4bb] Rmerge of the last shell is zero
Dear All, Here are some more details about the question I asked earlier about Rmerge is 0 in the last shell. I processed the data using HKL2000. The space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back the resolution any more. But I don't know how to explain Rmerge in the last shell being 0. Besides, I am wondering if this data is publishable (with Rmerge being 0 in the last shell). Thank you so much for your help! Best, Yafang On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.comwrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907
Re: [ccp4bb] Rmerge of the last shell is zero
Hello Yafang, The answer lies in the fact that you used HKL2000. Scalepack has a long standing feature where it reports Rmerge 100% as zero. Quite why they do that is a mystery, but your Rmerge in the outermost shell is NOT zero - the Rmerge for the lower resolution shells will show up as non-zero if Rmerge 100%. That feature is overdue for a fix. Alternatively export your scaled data with NO MERGE ORIGINAL INDEX and import into CCP4 via Pointless and have Scala or Aimless report the correct statistics. Reprocessing the data using XDS or Mosflm will ultimately lead you to scaling the data with a program that doesn't have that bug. If you do this, report Rmeas rather than Rmerge, the former being a better measure. Phil Jeffrey Princeton From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen [yafangche...@gmail.com] Sent: Wednesday, August 14, 2013 11:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rmerge of the last shell is zero Dear All, Here are some more details about the question I asked earlier about Rmerge is 0 in the last shell. I processed the data using HKL2000. The space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back the resolution any more. But I don't know how to explain Rmerge in the last shell being 0. Besides, I am wondering if this data is publishable (with Rmerge being 0 in the last shell). Thank you so much for your help! Best, Yafang On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.commailto:yafangche...@gmail.com wrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907
Re: [ccp4bb] Rmerge of the last shell is zero
HKL2000 sets to 0 the Rmerge in any shell where it is higher than 100% OUCH Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen [yafangche...@gmail.com] Sent: 14 August 2013 16:32 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rmerge of the last shell is zero Dear All, Here are some more details about the question I asked earlier about Rmerge is 0 in the last shell. I processed the data using HKL2000. The space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back the resolution any more. But I don't know how to explain Rmerge in the last shell being 0. Besides, I am wondering if this data is publishable (with Rmerge being 0 in the last shell). Thank you so much for your help! Best, Yafang On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.commailto:yafangche...@gmail.com wrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907
Re: [ccp4bb] Rmerge of the last shell is zero
No matter what the value printed out for Rmerge in the outer shell is, I recommend using - or n/a in your paper. This is because sum(|I-I0|)/sum(I) actually is equal to n/a when sum(I) = 0. -James Holton MAD Scientist On Wed, Aug 14, 2013 at 8:41 AM, Pietro Roversi pietro.rove...@bioch.ox.ac.uk wrote: HKL2000 sets to 0 the Rmerge in any shell where it is higher than 100% OUCH Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen [yafangche...@gmail.com] Sent: 14 August 2013 16:32 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rmerge of the last shell is zero Dear All, Here are some more details about the question I asked earlier about Rmerge is 0 in the last shell. I processed the data using HKL2000. The space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back the resolution any more. But I don't know how to explain Rmerge in the last shell being 0. Besides, I am wondering if this data is publishable (with Rmerge being 0 in the last shell). Thank you so much for your help! Best, Yafang On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.com mailto:yafangche...@gmail.com wrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907
Re: [ccp4bb] Rmerge of the last shell is zero
This HKL2000 (scalepack) feature is actually extremely sensible: an Rmerge that high is mathematically meaningless, it quite literally tells you nothing at all about he signal in your data. So I second James's advice: just put n/a in your table 1. If the reviewer complains, point them to Karplus Diederichs, Science, 2012, and Evans and Murshudov, ActaD, 2013, and tell them to join us in the 21st century. On 14/08/2013 16:41, Jeffrey, Philip D. wrote: Hello Yafang, The answer lies in the fact that you used HKL2000. Scalepack has a long standing feature where it reports Rmerge 100% as zero. Quite why they do that is a mystery, but your Rmerge in the outermost shell is NOT zero - the Rmerge for the lower resolution shells will show up as non-zero if Rmerge 100%. That feature is overdue for a fix. Alternatively export your scaled data with NO MERGE ORIGINAL INDEX and import into CCP4 via Pointless and have Scala or Aimless report the correct statistics. Reprocessing the data using XDS or Mosflm will ultimately lead you to scaling the data with a program that doesn't have that bug. If you do this, report Rmeas rather than Rmerge, the former being a better measure. Phil Jeffrey Princeton *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen [yafangche...@gmail.com] *Sent:* Wednesday, August 14, 2013 11:32 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Rmerge of the last shell is zero Dear All, Here are some more details about the question I asked earlier about Rmerge is 0 in the last shell. I processed the data using HKL2000. The space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back the resolution any more. But I don't know how to explain Rmerge in the last shell being 0. Besides, I am wondering if this data is publishable (with Rmerge being 0 in the last shell). Thank you so much for your help! Best, Yafang On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.com mailto:yafangche...@gmail.com wrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907
Re: [ccp4bb] Rmerge of the last shell is zero
But it is highly unlikely that sum(I) in the denominator is zero if I/sig(I) is 2 as reported (providing the sig(I) is valid- what was chi^2 in the last shell and overall?). I sort of disagree that R-merge values over 1.0 are meaningless, provided not too far over. Granted R-meas is more meaningful, but with high redundancy R-merge approximates R-meas, and R-merge is what the PDB is accepting now. A value a little over 1 tells you the standard deviation of the individual mesurements is a little larger than the average signal in those measurements. Understanding a little about distribution of intensities and error propogation (standard error of the mean, R-pim) the user will understand that quite a few reflections were stronger than this standard deviation, and that the error in the averaged intensities is be less than this standard deviation, and not have a problem. The problem comes with the 100%-sum mentality which says that if your error is 100% the signal must be zero%. That is why I don't like to express R-whatever as a percent. If the signal was really zero, R-merge or R-meas would be plus/minus infinity. So much for 100%-sum. So rerun scalepack with no merge original index, reprocess through CCp4 or just rune Diedrich's rmerge program or phenix.merging_statistics to get the value of r-merge (and r-meas and R-pim and cc1/2) from the .sca file. If it is much over 3 than I would rexamine the I/sig(I) value (which can be misestimated) and consider discarding the last shell. If it is 3 or less, report it. The PDB ADDIT2 application used to not accept values over .99, but you can put that and ask the friendly annotator to correct it in the final PDB file. If the annotator objects, THEN point (him) to the 2012 KD paper- R-meas in the last shell there was over 4, and they concluded there was useful information. Of course by then you will have refined your structure, and unbiased R-free in the last shell can be a good indicator. If you refine once in phenix you can use phenix.cc_star to calculate cc* and compare with R and R-free; from the output mtz file and your unmerged .sca file. eab Frank von Delft wrote: This HKL2000 (scalepack) feature is actually extremely sensible: an Rmerge that high is mathematically meaningless, it quite literally tells you nothing at all about he signal in your data. So I second James's advice: just put n/a in your table 1. If the reviewer complains, point them to Karplus Diederichs, Science, 2012, and Evans and Murshudov, ActaD, 2013, and tell them to join us in the 21st century. On 14/08/2013 16:41, Jeffrey, Philip D. wrote: Hello Yafang, The answer lies in the fact that you used HKL2000. Scalepack has a long standing feature where it reports Rmerge 100% as zero. Quite why they do that is a mystery, but your Rmerge in the outermost shell is NOT zero - the Rmerge for the lower resolution shells will show up as non-zero if Rmerge 100%. That feature is overdue for a fix. Alternatively export your scaled data with NO MERGE ORIGINAL INDEX and import into CCP4 via Pointless and have Scala or Aimless report the correct statistics. Reprocessing the data using XDS or Mosflm will ultimately lead you to scaling the data with a program that doesn't have that bug. If you do this, report Rmeas rather than Rmerge, the former being a better measure. Phil Jeffrey Princeton *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen [yafangche...@gmail.com] *Sent:* Wednesday, August 14, 2013 11:32 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Rmerge of the last shell is zero Dear All, Here are some more details about the question I asked earlier about Rmerge is 0 in the last shell. I processed the data using HKL2000. The space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back the resolution any more. But I don't know how to explain Rmerge in the last shell being 0. Besides, I am wondering if this data is publishable (with Rmerge being 0 in the last shell). Thank you so much for your help! Best, Yafang On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen yafangche...@gmail.com mailto:yafangche...@gmail.com wrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 -- Yafang Chen Graduate Research Assistant Mesecar Lab Department
Re: [ccp4bb] Rmerge of the last shell is zero
On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry ber...@upstate.eduwrote: If you refine once in phenix you can use phenix.cc_star to calculate cc* and compare with R and R-free; from the output mtz file and your unmerged .sca file. FYI, this should also work with structures refined in Refmac, assuming it can recalculate the R-factors to within a reasonable margin of error. -Nat
