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:[log in to unmask]]
> Sent: Tuesday, December 20, 2016 15:46
> To: Robbie Joosten <[log in to unmask]>; CCP4BB
> <[log in to unmask]>
> 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:[log in to unmask]>
> Verzonden: dinsdag 20 december 2016 14:23
> Aan: [log in to unmask] <mailto:[log in to unmask]>
> Onderwerp: Re: [ccp4bb] Calculation of generalised R-factor?
>
>
>
>
> I'd be interested as well.
>
> JPK
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On
> Behalf Of Dirk Kostrewa
> Sent: Tuesday, December 20, 2016 8:47 AM
> To: [log in to unmask] <mailto:[log in to unmask]>
> 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: [log in to unmask]
> <mailto:[log in to unmask]>
> 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: [log in to unmask]
> <mailto:[log in to unmask]>
> WWW: www.genzentrum.lmu.de <http://www.genzentrum.lmu.de>
> *******************************************************
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