Re: [ccp4bb] PHENIX & BSS refinement

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

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Subject: Re: ccp4 6.1.0 with macbookpro
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2009-02-04

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

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

Previous message:
Subject: Re: ccp4 6.1.0 with macbookpro
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2009-02-04

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