Re: [ccp4bb] PDB redo and biased/unbiased R-free
Hi Nadia, Ethan is quite right. R(free,unbiased) is explained in more detail in this paper (https://pdb-redo.eu/publications/CCP42011.pdf) and some of the references. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Ethan Merritt > Sent: Tuesday, February 06, 2018 23:59 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] PDB redo and biased/unbiased R-free > > On Tuesday, 06 February 2018 17:25:13 Nadia Leloup wrote: > > Dear all, > > > > I was looking at a 3 angstrom structure from 2015 with relatively bad > > statistics, so I decided to look at the pdb-redo of said structure. > > Surprisingly, pdb-redo statistics are even worse. > > You say "even worse", but the subset of statistics you show does not look so > bad for a 3A structure either before or after re-refinement. > Other than maybe the Rfree itself, which is what you ask about. > > > As you can see on the > > attached picture, the pdb-redo Rfree comes with a caveat: > > > > R-free was considered biased, the estimated unbiased R-free was used > > > > I understand that the R-free was considered biased because a new > > (Rfree) test set was determined. However, I'm not sure what is the > > unbiased R-free is / how it is calculated in this case? > > From the "How does it work" page on the PDB Redo web site, my > understanding is that rather than calculating Rfree from the re-refinement, > various other quality measures are used to calculate an expected Rfree/R > ratio consistent with other structures of similar quality. > This ratio is then multipled by R to yield an estimated Rfree. > > Robbie Joosten will probably correct me if I have that wrong :-) > > cheers, > > Ethan > > > > > Thanks in advance, > > > > Best, > > > > Nadia > > -- > Ethan A Merritt, Dept of Biochemistry > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] PDB redo and biased/unbiased R-free
On Tuesday, 06 February 2018 17:25:13 Nadia Leloup wrote: > Dear all, > > I was looking at a 3 angstrom structure from 2015 with relatively bad > statistics, so I decided to look at the pdb-redo of said structure. > Surprisingly, pdb-redo statistics are even worse. You say "even worse", but the subset of statistics you show does not look so bad for a 3A structure either before or after re-refinement. Other than maybe the Rfree itself, which is what you ask about. > As you can see on the > attached picture, the pdb-redo Rfree comes with a caveat: > > R-free was considered biased, the estimated unbiased R-free was used > > I understand that the R-free was considered biased because a new (Rfree) > test set was determined. However, I'm not sure what is the unbiased R-free > is / how it is calculated in this case? >From the "How does it work" page on the PDB Redo web site, my understanding is that rather than calculating Rfree from the re-refinement, various other quality measures are used to calculate an expected Rfree/R ratio consistent with other structures of similar quality. This ratio is then multipled by R to yield an estimated Rfree. Robbie Joosten will probably correct me if I have that wrong :-) cheers, Ethan > > Thanks in advance, > > Best, > > Nadia -- Ethan A Merritt, Dept of Biochemistry Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
[ccp4bb] PDB redo and biased/unbiased R-free
Dear all, I was looking at a 3 angstrom structure from 2015 with relatively bad statistics, so I decided to look at the pdb-redo of said structure. Surprisingly, pdb-redo statistics are even worse. As you can see on the attached picture, the pdb-redo Rfree comes with a caveat: R-free was considered biased, the estimated unbiased R-free was used I understand that the R-free was considered biased because a new (Rfree) test set was determined. However, I'm not sure what is the unbiased R-free is / how it is calculated in this case? Thanks in advance, Best, Nadia
