Re: [ccp4bb] CC-half value ??
Thank you for your valuable suggestions..it really helped me a lot.. On Fri, Aug 15, 2014 at 8:38 PM, Phil Evans wrote: > I should make the estimation in Aimless more robust, and curve fitting > sounds like a good idea (but what function?). Outliers are a difficult > problem, but anyway I think you should look at the curve and not just the > number estimated. I would look at I/sigI as well, and anisotropy to decide > the resolution. However, the final cutoff should probably be based on > refinement, and also I don't think the exact cutoff makes a huge difference > (see http://www.ncbi.nlm.nih.gov/pubmed/23793146) > > Phil > > On 15 Aug 2014, at 15:54, Ed Pozharski wrote: > > > Same here. Ultimately, the KD test must be used in the end to finalize > the resolution (keeping in mind recently discussed issues of effective > resolution given data completeness). I just want to add that at least some > versions of aimless report overestimated resolution based on CC1/2 cutoff > when outliers are present (e.g. due to ice rings or salt diffraction). It > seems that aimless just picks the highest resolution bin where cc1/2> 0.5 > even if some lower resolution bins are below 0.5 as well. I have written a > script for more robust automated evaluation of these curves. In a > nutshell, it fits CC1/2 (d) curve to 1/(1+exp (-x)) and returns the > resolution at midpoint. I'm pretty sure that theoretical CC1/2 (d) > dependence is different from this, but it seems good enough for a rough > estimate. > > > > > > Sent on a Sprint Samsung Galaxy S® III > > > > > > > > > > > > > > > > > > ---- Original message > > From: Roger Rowlett > > Date:08/14/2014 5:44 PM (GMT-05:00) > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] CC-half value ?? > > > > Exactly. Aimless will give you suggested resolution cutoffs based on CC > 1/2 in the log file. > > > > Roger Rowlett > > > > On Aug 14, 2014 5:04 PM, "conan仙人指路" wrote: > > Hi Faisal, > > > > CC-half standard is valuable in evaluating the cut-off of highest > resolution. Sometimes even if I/sigI is close to 1 and completeness is not > as high, if CC-half is still significant, it may be worth incorporate the > extra high-res shell data and extend the resolution. Again, if only the > reliability and unbias are carefully confirmed, and the apparent > significant CC-half is not due to an artifact of some other factors like > ice ring etc. > > (Ref: Karplus PA and Diederichs K. 2012 Science 336, 1030-1033 > https://www.pubmed.com/pubmed/22628654) > > > > It has yet to be appreciated by most population of the crystallography > society, unlike the I/sigI, completeness, Rsym. In particular, Rsym has > gradually less a direct measurement of the data quality and or determinant > of resolution cut-off. > > > > Best, > > Conan > > > > Hongnan Cao, Ph.D. > > Department of Biochemistry > > Rice University > > > > Date: Fri, 15 Aug 2014 01:39:48 +0530 > > From: faisaltari...@gmail.com > > Subject: [ccp4bb] CC-half value ?? > > To: CCP4BB@JISCMAIL.AC.UK > > > > Dear all > > > > How CC-half value of a data set determines the maximum resolution limit > during data processing ?? Although much we know about the Rsym and I/Isig > values of the highest resolution shell while processing the data, what are > the parameters we need to check related to CC-half values ?? > > > > -- > > Regards > > > > Faisal > > School of Life Sciences > > JNU > > > -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] CC-half value ??
I should make the estimation in Aimless more robust, and curve fitting sounds like a good idea (but what function?). Outliers are a difficult problem, but anyway I think you should look at the curve and not just the number estimated. I would look at I/sigI as well, and anisotropy to decide the resolution. However, the final cutoff should probably be based on refinement, and also I don't think the exact cutoff makes a huge difference (see http://www.ncbi.nlm.nih.gov/pubmed/23793146) Phil On 15 Aug 2014, at 15:54, Ed Pozharski wrote: > Same here. Ultimately, the KD test must be used in the end to finalize the > resolution (keeping in mind recently discussed issues of effective resolution > given data completeness). I just want to add that at least some versions of > aimless report overestimated resolution based on CC1/2 cutoff when outliers > are present (e.g. due to ice rings or salt diffraction). It seems that > aimless just picks the highest resolution bin where cc1/2> 0.5 even if some > lower resolution bins are below 0.5 as well. I have written a script for more > robust automated evaluation of these curves. In a nutshell, it fits CC1/2 > (d) curve to 1/(1+exp (-x)) and returns the resolution at midpoint. I'm > pretty sure that theoretical CC1/2 (d) dependence is different from this, but > it seems good enough for a rough estimate. > > > Sent on a Sprint Samsung Galaxy S® III > > > > > > > > > Original message > From: Roger Rowlett > Date:08/14/2014 5:44 PM (GMT-05:00) > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] CC-half value ?? > > Exactly. Aimless will give you suggested resolution cutoffs based on CC 1/2 > in the log file. > > Roger Rowlett > > On Aug 14, 2014 5:04 PM, "conan仙人指路" wrote: > Hi Faisal, > > CC-half standard is valuable in evaluating the cut-off of highest > resolution. Sometimes even if I/sigI is close to 1 and completeness is not as > high, if CC-half is still significant, it may be worth incorporate the extra > high-res shell data and extend the resolution. Again, if only the reliability > and unbias are carefully confirmed, and the apparent significant CC-half is > not due to an artifact of some other factors like ice ring etc. > (Ref: Karplus PA and Diederichs K. 2012 Science 336, 1030-1033 > https://www.pubmed.com/pubmed/22628654) > > It has yet to be appreciated by most population of the crystallography > society, unlike the I/sigI, completeness, Rsym. In particular, Rsym has > gradually less a direct measurement of the data quality and or determinant of > resolution cut-off. > > Best, > Conan > > Hongnan Cao, Ph.D. > Department of Biochemistry > Rice University > > Date: Fri, 15 Aug 2014 01:39:48 +0530 > From: faisaltari...@gmail.com > Subject: [ccp4bb] CC-half value ?? > To: CCP4BB@JISCMAIL.AC.UK > > Dear all > > How CC-half value of a data set determines the maximum resolution limit > during data processing ?? Although much we know about the Rsym and I/Isig > values of the highest resolution shell while processing the data, what are > the parameters we need to check related to CC-half values ?? > > -- > Regards > > Faisal > School of Life Sciences > JNU >
Re: [ccp4bb] CC-half value ??
Same here. Ultimately, the KD test must be used in the end to finalize the resolution (keeping in mind recently discussed issues of effective resolution given data completeness). I just want to add that at least some versions of aimless report overestimated resolution based on CC1/2 cutoff when outliers are present (e.g. due to ice rings or salt diffraction). It seems that aimless just picks the highest resolution bin where cc1/2> 0.5 even if some lower resolution bins are below 0.5 as well. I have written a script for more robust automated evaluation of these curves. In a nutshell, it fits CC1/2 (d) curve to 1/(1+exp (-x)) and returns the resolution at midpoint. I'm pretty sure that theoretical CC1/2 (d) dependence is different from this, but it seems good enough for a rough estimate. Sent on a Sprint Samsung Galaxy S® III Original message From: Roger Rowlett Date:08/14/2014 5:44 PM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CC-half value ?? Exactly. Aimless will give you suggested resolution cutoffs based on CC 1/2 in the log file. Roger Rowlett On Aug 14, 2014 5:04 PM, "conan仙人指路" wrote: Hi Faisal, CC-half standard is valuable in evaluating the cut-off of highest resolution. Sometimes even if I/sigI is close to 1 and completeness is not as high, if CC-half is still significant, it may be worth incorporate the extra high-res shell data and extend the resolution. Again, if only the reliability and unbias are carefully confirmed, and the apparent significant CC-half is not due to an artifact of some other factors like ice ring etc. (Ref: Karplus PA and Diederichs K. 2012 Science 336, 1030-1033 https://www.pubmed.com/pubmed/22628654) It has yet to be appreciated by most population of the crystallography society, unlike the I/sigI, completeness, Rsym. In particular, Rsym has gradually less a direct measurement of the data quality and or determinant of resolution cut-off. Best, Conan Hongnan Cao, Ph.D. Department of Biochemistry Rice University Date: Fri, 15 Aug 2014 01:39:48 +0530 From: faisaltari...@gmail.com Subject: [ccp4bb] CC-half value ?? To: CCP4BB@JISCMAIL.AC.UK Dear all How CC-half value of a data set determines the maximum resolution limit during data processing ?? Although much we know about the Rsym and I/Isig values of the highest resolution shell while processing the data, what are the parameters we need to check related to CC-half values ?? -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] CC-half value ??
Exactly. Aimless will give you suggested resolution cutoffs based on CC 1/2 in the log file. Roger Rowlett On Aug 14, 2014 5:04 PM, "conan仙人指路" wrote: > Hi Faisal, > > CC-half standard is valuable in evaluating the cut-off of highest > resolution. Sometimes even if I/sigI is close to 1 and completeness is not > as high, if CC-half is still significant, it may be worth incorporate the > extra high-res shell data and extend the resolution. Again, if only the > reliability and unbias are carefully confirmed, and the apparent > significant CC-half is not due to an artifact of some other factors like > ice ring etc. > (Ref: Karplus PA and Diederichs K. 2012 Science 336, 1030-1033 > https://www.pubmed.com/pubmed/22628654) > > It has yet to be appreciated by most population of the crystallography > society, unlike the I/sigI, completeness, Rsym. In particular, Rsym has > gradually less a direct measurement of the data quality and or determinant > of resolution cut-off. > > Best, > Conan > > Hongnan Cao, Ph.D. > Department of Biochemistry > Rice University > > -- > Date: Fri, 15 Aug 2014 01:39:48 +0530 > From: faisaltari...@gmail.com > Subject: [ccp4bb] CC-half value ?? > To: CCP4BB@JISCMAIL.AC.UK > > Dear all > > How CC-half value of a data set determines the maximum resolution limit > during data processing ?? Although much we know about the Rsym and I/Isig > values of the highest resolution shell while processing the data, what are > the parameters we need to check related to CC-half values ?? > > -- > Regards > > Faisal > School of Life Sciences > JNU > >
Re: [ccp4bb] CC-half value ??
Hi Faisal, CC-half standard is valuable in evaluating the cut-off of highest resolution. Sometimes even if I/sigI is close to 1 and completeness is not as high, if CC-half is still significant, it may be worth incorporate the extra high-res shell data and extend the resolution. Again, if only the reliability and unbias are carefully confirmed, and the apparent significant CC-half is not due to an artifact of some other factors like ice ring etc.(Ref: Karplus PA and Diederichs K. 2012 Science 336, 1030-1033 https://www.pubmed.com/pubmed/22628654) It has yet to be appreciated by most population of the crystallography society, unlike the I/sigI, completeness, Rsym. In particular, Rsym has gradually less a direct measurement of the data quality and or determinant of resolution cut-off. Best,Conan Hongnan Cao, Ph.D.Department of BiochemistryRice University Date: Fri, 15 Aug 2014 01:39:48 +0530 From: faisaltari...@gmail.com Subject: [ccp4bb] CC-half value ?? To: CCP4BB@JISCMAIL.AC.UK Dear all How CC-half value of a data set determines the maximum resolution limit during data processing ?? Although much we know about the Rsym and I/Isig values of the highest resolution shell while processing the data, what are the parameters we need to check related to CC-half values ?? -- Regards Faisal School of Life Sciences JNU
[ccp4bb] CC-half value ??
Dear all How CC-half value of a data set determines the maximum resolution limit during data processing ?? Although much we know about the Rsym and I/Isig values of the highest resolution shell while processing the data, what are the parameters we need to check related to CC-half values ?? -- Regards Faisal School of Life Sciences JNU
[ccp4bb] CC-half value
Dear all How CC-half value of a data set determines the resolution limit for the data processing ?? Although much we know about the Rsym and I/Isig values of the highest resolution shell while processing the data, what are the parameters we need to check related to CC-half values ?? -- Regards Faisal School of Life Sciences JNU
