Re: [ccp4bb] Valid to stop Refmac after TLS refinement?

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Drug Discovery & Development - eCheminfo Autumn meeting, program, CFP, bursary awards
From: barry {- dot -} hardy {- at -} TELE2 {- dot -} CH barry {- dot -} hardy {- at -} TELE2 {- dot -} CH
Date: 2007-03-28

Next message:
Subject: Re: phasing power ofatoms
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-03-28

Subject: Re: Valid to stop Refmac after TLS refinement?
From: "NM Burton, Biochemistry" Nick {- dot -} Burton {- at -} BRISTOL {- dot -} AC {- dot -} UK
Date: 2007-03-28

Hello,

The first kind replies have reminded me that I should have included
information on the Refmac weighting term - it's set at 0.1, and the RMSD
bonds/angles is 0.016/1.6 after Refmac co-ordinate refinement. So I'm
assuming that is not the problem. And I made sure to keep the same Rfree
set.

Thanks again,

Nick

--On 28 March 2007 16:34 +0100 "NM Burton, Biochemistry"
wrote:

> Hello,
>
> I've refined a structure with CNS to Rwork/free=0.226/0.273. I switched
> to Refmac5.2 to take advantage of TLS refinement and set up a run with 10
> cycles of TLS refinement (groups as suggested by the TLSMD server)
> followed by 10 cycles of restrained co-ordinate refinement. After the
> TLS cycles the model was improved (Rwork/free=0.222/0.241), however
> during co-ordinate refinement Rfree refined up (final
> Rwork/free=0.197/0.264). My understanding would be that the TLS
> refinement is modelling the ADPs most accurately, but that Refmac's
> co-ordinate refinement is over-fitting slightly. Would this seem
> correct? And if so, is it valid to run Refmac with no cycles of
> co-ordinate refinement and take the resulting model as the final
> structure?
>
> Thanks very much,
>
> Nick
>
> ----------------------
> NM Burton, Biochemistry
> Nick.Burton@bristol.ac.uk

----------------------
NM Burton, Biochemistry
Nick.Burton@bristol.ac.uk

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: Re: phasing power ofatoms
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-03-28