Re: [ccp4bb] PHENIX & BSS refinement

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

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From: Eric Liu erictaoranliu19971997 {- at -} GMAIL {- dot -} COM
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From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-02-04

Subject: Re: PHENIX & BSS refinement
From: Miguel Ortiz Lombardia miguel {- dot -} ortiz-lombardia {- at -} AFMB {- dot -} UNIV-MRS {- dot -} FR
Date: 2009-02-04

Hi Pavel,

Thanks, it is clear now.
I have a last concern, though. Does phenix impose minimal values to
the refined ADPs? I guess it does not, for I have found nothing like
that in the documentation. But, if it does so, are they imposed to the
individual B-factors or the B-overall is also taken into account? In
the former case you might have problems with the refinement in a case
as the one I described in my previous e-mail (coming from a model with
artificially low, 'residual' B-factors).

Cheers,

Miguel

Le 4 févr. 09 à 18:23, Pavel Afonine a écrit :

> Hi Miguel,
>
>> Right, but why this happens only in the final bss step ? Why not in
>> the first one?
>
> It's arbitrary: one can do it every macro-cycle as well. The main
> idea is to have a total B-factor in ATOM records written out to a
> PDB file.
>
>> I have noticed the behaviour described by José when I refine in
>> phenix a model previously refined in refmac5 _with_ TLS, so the
>> ADPs in the model are actually 'residual' ADPs of refmac5 TLS
>> refinement. In these cases, during the refinement in phenix, the
>> ADPs seem to be kept at very low values all throughout until they
>> abruptly go to the higher, more reasonable values, after the final
>> bulk solvent correction step. There may be a good reason for this
>> behaviour, but I don't see it. I would appreciate if you could
>> elaborate.
>
> Like I said, it is arbitrary. You can store the overall B-factor in
> overall anisotropic scale matrix (B_overall) or in individual atomic
> B-factors; in both cases the total model structure factor
> Fmodel = scale_overall * exp(-h*B_overall*ht) * (Fcalc + k_sol *
> exp(-B_sol*s^2) * Fmask)
> will remain the same.
>
> Pavel.
>
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--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
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13288 Marseille cedex 9
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Tel : +33(0) 491 82 55 93
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e-mail: miguel.ortiz-lombardia@afmb.univ-mrs.fr
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: song CRT Multiscan E540 monitor for stereo view
From: Eric Liu erictaoranliu19971997 {- at -} GMAIL {- dot -} COM
Date: 2009-02-04

Next message:
Subject: Re: PHENIX & BSS refinement
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-02-04