[ccp4bb] Why TLS refinement may go wrong and why it is so often the case (was: Re: [ccp4bb] Calculation of generalised R-factor?)

2016-12-22 Thread Pavel Afonine
Dear Ethan, thanks for comments. I do remember we talked about it last year in Argonne at CCP4 school and we did not seem to agree indeed. Let me bring my arguments as you stated yours. Refinement is an optimization problem that involves model, data and fitting tools (such as target function and

[ccp4bb] Fwd: [ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Dirk Kostrewa
Dear CCP4ers, many thanks to all of you who replied to my request! I wish you a Merry Christmas and a Happy New Year! Dirk. Forwarded Message Subject:[ccp4bb] Calculation of generalised R-factor? Date: Tue, 20 Dec 2016 14:47:00 +0100 From: Dirk Kostrewa <ko

Re: [ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Ethan Merritt
On Tuesday, 20 December 2016 10:28:44 PM Pavel Afonine wrote: > Hi Dirk, > > > 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

Re: [ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Pavel Afonine
Hi Dirk, 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

Re: [ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Robbie Joosten
uesday, 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

Re: [ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Dirk Kostrewa
to: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.A

Re: [ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Robbie Joosten
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 generali

Re: [ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Keller, Jacob
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

[ccp4bb] Calculation of generalised R-factor?

2016-12-20 Thread Dirk Kostrewa
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