Re: [ccp4bb] TLS refinement

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

Previous message:
Subject: TLS refinement
From: "Nalam, Madhavi" Madhavi {- dot -} Nalam {- at -} UMASSMED {- dot -} EDU
Date: 2009-03-03

Next message:
Subject: Re: shape complementarity calculations
From: Mike Lawrence lawrence {- at -} WEHI {- dot -} EDU {- dot -} AU
Date: 2009-03-03

Subject: Re: TLS refinement
From: Ethan A Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2009-03-03

On Tuesday 03 March 2009, Nalam, Madhavi wrote:
> Hello:
> I am trying to refine a structure at 3 A resolution using TLS refinement. After 8-10 cycles of TLS refinement, R-free and R-factor converges. But R-free starts going up again from the first round of restrained refinement. My question now is can I stop just after TLS refinement without doing any restrained refinement?

In the "Refinement Parameters" panel of the ccp4i interface to refmac5, select
'refine _overall_ temperature factors' rather than 'refine _isotropic_ temperature factors'.

> If so, the PDB file contains ANISOU cards for the atoms. Does this mean anisotropic refinement is performed on the atoms which should not be the case for a 3 A structure?

No. The ANISOU records contain the Uij approximation to the result of applying
your TLS model to each atom.

> Thanks in advance,
> Regards,
> Madhavi
>
>
> ________________________________
>
> From: CCP4 bulletin board on behalf of Edward A. Berry
> Sent: Tue 3/3/2009 5:39 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] shape complementarity calculations - oops!
>
>
>
> Oganesyan, Vaheh wrote:
>
> > Among non-runnable programs in CCP4 there is the sc program that indeed
> > does not run.
> >
>
> Sorry, I didn't see the rest of your post.
> I had sc running and producing meaningful results back in 2006-2007,
> I can check which version etc.
>
> Ed
>
>
>
>

--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

CCP4bb navigation

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

Previous message:
Subject: TLS refinement
From: "Nalam, Madhavi" Madhavi {- dot -} Nalam {- at -} UMASSMED {- dot -} EDU
Date: 2009-03-03

Next message:
Subject: Re: shape complementarity calculations
From: Mike Lawrence lawrence {- at -} WEHI {- dot -} EDU {- dot -} AU
Date: 2009-03-03