Dear Robbie,
thanks for your reply. According to the REFMAC5 manual, the weighted
R-factor is just:
weighted R factor = sum w ||F_o -|F_c ||/sum w |F_o |
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
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
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
WWW: www.genzentrum.lmu.de
*******************************************************
