Re: [ccp4bb] PDB redo R free
To add to Tim's references, the algorithms that pdb-redo uses to deal with Rfree and possible bias are described here: https://journals.iucr.org/d/issues/2012/04/00/ba5174/index.htmlIf you happen to have a very small dataset (< 5000 reflections) pdb-redo does 10-fold cross validation and returns Rcomplete as well.Cheers,RobbieOn 28 Apr 2023 11:26, Tim Gruene wrote:Dear Qixu Cai, it is a misconception that Rfree was not free anymore. The gap does not close when you swap the reflections in Rfree set. The 'free' reflections are freed when you do proper refinement, i.e., when the value of the target function becomes stationary. See https://doi.org/10.1107/S0907444997013875 and https://doi.org/10.1107/S0907444999016868 for the mathematical background, https://doi.org/10.1073/pnas.1502136112 for an experimental treatment, and Ian Tickle's explanations on this topic here on the CCP4bb. Best wishes, Tim On Fri, 28 Apr 2023 16:54:07 +0800 Qixu Cai wrote: > Dear Robbie and Tim， > > Thanks a lot for your reply. I just do not understand that if we can > change the R free set during different rounds of refinement, the gap > between Rwork and Rfree would be small, and Rfree would be > meaningless, as R-free set is not "free". > > Best regards, > > Qixu Cai > Email: caiq...@gmail.com > > > > Robbie Joosten 于2023年4月28日周五 > 15:26写道： > > > Hi Qixu, > > > > PDB-REDO tries to have a minimum number test set reflections to > > reduce the error margin in R-free. As Tim says this is not a > > problem but if you reach out privately we can change your > > calculation to use your current testset. That is not recommended > > though. > > > > Cheers, > > Robbie > > > > On 28 Apr 2023 04:51, Qixu Cai wrote: > > > > Dear all, > > > > I'm using the PDB-REDO server to refine my structure. I found that > > PDB-REDO said that 5% R-free set is too small and it created a new > > R-free set. > > > > Is possible for the PDB-REDO server to keep the original R-free set > > to make final Rfree value comparable? > > > > Best regards, > > > > Qixu Cai > > Email: caiq...@gmail.com > > > > > > -- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > > -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
Re: [ccp4bb] PDB redo R free
Dear Qixu Cai, it is a misconception that Rfree was not free anymore. The gap does not close when you swap the reflections in Rfree set. The 'free' reflections are freed when you do proper refinement, i.e., when the value of the target function becomes stationary. See https://doi.org/10.1107/S0907444997013875 and https://doi.org/10.1107/S0907444999016868 for the mathematical background, https://doi.org/10.1073/pnas.1502136112 for an experimental treatment, and Ian Tickle's explanations on this topic here on the CCP4bb. Best wishes, Tim On Fri, 28 Apr 2023 16:54:07 +0800 Qixu Cai wrote: > Dear Robbie and Tim， > > Thanks a lot for your reply. I just do not understand that if we can > change the R free set during different rounds of refinement, the gap > between Rwork and Rfree would be small, and Rfree would be > meaningless, as R-free set is not "free". > > Best regards, > > Qixu Cai > Email: caiq...@gmail.com > > > > Robbie Joosten 于2023年4月28日周五 > 15:26写道： > > > Hi Qixu, > > > > PDB-REDO tries to have a minimum number test set reflections to > > reduce the error margin in R-free. As Tim says this is not a > > problem but if you reach out privately we can change your > > calculation to use your current testset. That is not recommended > > though. > > > > Cheers, > > Robbie > > > > On 28 Apr 2023 04:51, Qixu Cai wrote: > > > > Dear all, > > > > I'm using the PDB-REDO server to refine my structure. I found that > > PDB-REDO said that 5% R-free set is too small and it created a new > > R-free set. > > > > Is possible for the PDB-REDO server to keep the original R-free set > > to make final Rfree value comparable? > > > > Best regards, > > > > Qixu Cai > > Email: caiq...@gmail.com > > > > > > -- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > > -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ pgpjj_Lr7i04I.pgp Description: OpenPGP digital signature
Re: [ccp4bb] PDB redo R free
Dear Robbie and Tim， Thanks a lot for your reply. I just do not understand that if we can change the R free set during different rounds of refinement, the gap between Rwork and Rfree would be small, and Rfree would be meaningless, as R-free set is not "free". Best regards, Qixu Cai Email: caiq...@gmail.com Robbie Joosten 于2023年4月28日周五 15:26写道： > Hi Qixu, > > PDB-REDO tries to have a minimum number test set reflections to reduce the > error margin in R-free. As Tim says this is not a problem but if you reach > out privately we can change your calculation to use your current testset. > That is not recommended though. > > Cheers, > Robbie > > On 28 Apr 2023 04:51, Qixu Cai wrote: > > Dear all, > > I'm using the PDB-REDO server to refine my structure. I found that > PDB-REDO said that 5% R-free set is too small and it created a new R-free > set. > > Is possible for the PDB-REDO server to keep the original R-free set to > make final Rfree value comparable? > > Best regards, > > Qixu Cai > Email: caiq...@gmail.com > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] PDB redo R free
Hi Qixu,PDB-REDO tries to have a minimum number test set reflections to reduce the error margin in R-free. As Tim says this is not a problem but if you reach out privately we can change your calculation to use your current testset. That is not recommended though.Cheers,RobbieOn 28 Apr 2023 04:51, Qixu Cai wrote:Dear all,I'm using the PDB-REDO server to refine my structure. I found that PDB-REDO said that 5% R-free set is too small and it created a new R-free set.Is possible for the PDB-REDO server to keep the original R-free set to make final Rfree value comparable?Best regards,Qixu CaiEmail: caiq...@gmail.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
Re: [ccp4bb] PDB redo R free
Dear Qixu Cai, the sets do not have to be identical, as long as refinement reaches a steady state. Best regards, Tim Am 28.04.2023 04:51, schrieb Qixu Cai: Dear all, I'm using the PDB-REDO server to refine my structure. I found that PDB-REDO said that 5% R-free set is too small and it created a new R-free set. Is possible for the PDB-REDO server to keep the original R-free set to make final Rfree value comparable? Best regards, Qixu Cai Email: caiq...@gmail.com - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
