Hi Dirk, You need the "Overall weighted R2 factor". The reference for the paper I meant is http://onlinelibrary.wiley.com/doi/10.1107/S0567739470000293/abstract
Cheers, Robbie > -----Original Message----- > From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] > Sent: Tuesday, December 20, 2016 15:46 > To: Robbie Joosten <robbie_joos...@hotmail.com>; CCP4BB > <ccp4bb@jiscmail.ac.uk> > Subject: Re: [ccp4bb] Calculation of generalised R-factor? > > Dear Robbie, > > > thanks for your reply. According to the REFMAC5 manual, the weighted R- > factor is just: > > > weighted R factor = sum w ||Fo-|Fc||/sum w |Fo| > > So, unfortunately, it is not the generalised R-factor. > > Do you have a reference for that follow-up paper? > > PDB_REDO does too much for my purpose ... > > Cheers, > > Dirk. > > > > On 20.12.2016 15:37, Robbie Joosten wrote: > > > The value for the Hamilton test is written by Refmac as the weighted > R-factor. There was a follow-up paper that showed that you shouldn’t use > the normal R-factor for the Hamilton test. > > > > PDB_REDO does the Hamilton test automatically, but you can also > feed two Refmac logfiles to the bselect program to do your own Hamilton > test. > > > > Cheers, > > Robbie > > > > Sent from my Windows 10 phone > > > > Van: Keller, Jacob <mailto:kell...@janelia.hhmi.org> > Verzonden: dinsdag 20 december 2016 14:23 > Aan: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > Onderwerp: Re: [ccp4bb] Calculation of generalised R-factor? > > > > > I'd be interested as well. > > JPK > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On > Behalf Of Dirk Kostrewa > Sent: Tuesday, December 20, 2016 8:47 AM > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > Subject: [ccp4bb] Calculation of generalised R-factor? > > Dear CCP4ers, > > I want to check the validity of the refinement of anisotropic B-factors > vs. TLS + isototropic B-factors using the Hamilton R-value ratio test as > described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol 68, > pp 468. This test uses the generalised R-factors (assuming unit weights), > RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that at the > end of refinement, one could also use the similar ratio of the usual R-factors, > I really would like to check the ratio of the RG-values after refinement. As far > as I can see, this value is not reported by the usual refinement programs. > > Is there a program that reads an mtz file with Fo and refined Fc and > just calculates RG? > > Best regards, > > Dirk. > > -- > > ******************************************************* > Dirk Kostrewa > Gene Center Munich, A5.07 > Department of Biochemistry > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > D-81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76998 > E-mail: kostr...@genzentrum.lmu.de > <mailto:kostr...@genzentrum.lmu.de> > WWW: www.genzentrum.lmu.de > <http://www.genzentrum.lmu.de> > ******************************************************* > > > > -- > > ******************************************************* > Dirk Kostrewa > Gene Center Munich, A5.07 > Department of Biochemistry > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > D-81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76998 > E-mail: kostr...@genzentrum.lmu.de > <mailto:kostr...@genzentrum.lmu.de> > WWW: www.genzentrum.lmu.de <http://www.genzentrum.lmu.de> > *******************************************************
