Re: [ccp4bb] PHENIX & BSS refinement

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

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Subject: Re: problem with ccp4 6.1.0 installation
From: Ronan Keegan ronan {- dot -} keegan {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-02-04

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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

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,

>
>> We have also seen that the B factor jumps up in this last step (see
>> bellow). Is anybody aware of this?
>
> This is because the trace of overall anisotropic scale matrix is
> added to atomic B-factors and subtracted from that matrix. This is
> exactly what CNS does (at least version 1.1).
>>

Right, but why this happens only in the final bss step ? Why not in
the first one?

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.

I was tempted to send this e-mail also to the phenixbb list in case
someone there could be interested... but cross-posting used to be
anathema :-)

Best regards,

Miguel
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombardia@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2

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CCP4bb navigation

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

Previous message:
Subject: Re: problem with ccp4 6.1.0 installation
From: Ronan Keegan ronan {- dot -} keegan {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-02-04

Next 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