Hmm...what causes Rmeas/pim to be the same like the linear Rmerge? This seems to be the case when the preceding term sum[sqrt(n/n-1)] =1 i.e. no redundancy? Somewhere here probably lies the source of discrepancy between mean I/Isig and linear Rmerge.
An explanation about the rationale of selecting processing cutoffs btw is in the link that Kay gave 3 weeks earlier: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/FAQ#why_do_the_la test_XDS.2FXSCALE_versions_only_give_a_single_table.2C_with_I.2Fsigma.3E.3D- 3_cutoff.3F BR -----Original Message----- From: Maia Cherney [mailto:ch...@ualberta.ca] Sent: Thursday, March 03, 2011 9:58 AM To: hofkristall...@gmail.com Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] I/sigmaI of >3.0 rule I see, there is no consensus about my data. Some people say 2.4A, other say all. Well, I chose 2.3 A. My rule was to be a little bit below Rmerg 100%. At 2.3A Rmerg was 98.7% Actually, I have published my paper in JMB. Yes, reviewers did not like that and even made me give Rrim and Rpim etc. Maia Bernhard Rupp (Hofkristallrat a.D.) wrote: > First of all I would ask a XDS expert for that because I don't know > exactly what stats the XDS program reports (shame on me, ok) nor what > the quality of your error model is, or what you want to use the data > for (I guess refinement - see Eleanor's response for that, and use all data). > > There is one point I'd like to make re cutoff: If one gets greedy and > collects too much noise in high resolution shells (like way below > <I/sigI> = > 0.8 or so) the scaling/integration may suffer from an overabundance of > nonsense data, and here I believe it makes sense to select a higher > cutoff (like what exactly?) and reprocess the data. Maybe one of our > data collection specialist should comment on that. > > BR > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Maia Cherney > Sent: Thursday, March 03, 2011 9:13 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] I/sigmaI of >3.0 rule > > I have to resend my statistics. > > Maia Cherney wrote: > >> Dear Bernhard >> >> I am wondering where I should cut my data off. Here is the statistics >> from XDS processing. >> >> Maia >> >> >>> >>> On 11-03-03 04:29 AM, Roberto Battistutta wrote: >>> >>> >>>> Dear all, >>>> I got a reviewer comment that indicate the "need to refine the >>>> structures >>>> >>>> >>> at an appropriate resolution (I/sigmaI of>3.0), and re-submit the >>> revised coordinate files to the PDB for validation.". In the >>> manuscript I present some crystal structures determined by molecular >>> replacement using the same protein in a different space group as >>> search model. Does anyone know the origin or the theoretical basis >>> of this "I/sigmaI>3.0" rule for an appropriate resolution? >>> >>> >>>> Thanks, >>>> Bye, >>>> Roberto. >>>> >>>> >>>> Roberto Battistutta >>>> Associate Professor >>>> Department of Chemistry >>>> University of Padua >>>> via Marzolo 1, 35131 Padova - ITALY tel. +39.049.8275265/67 fax. >>>> +39.049.8275239 roberto.battistu...@unipd.it >>>> www.chimica.unipd.it/roberto.battistutta/ >>>> VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 >>>> Padova - ITALY tel. +39.049.7923236 fax +39.049.7923250 www.vimm.it >>>> >>>> >>>> >>> >>> >> > > >
