[ccp4bb] Rant: B vs TLS, anisou, and PDB headers

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

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Subject: Re: [phenixbb] Rant: B vs TLS, anisou, and PDB headers
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-03-29

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Subject: Re: [phenixbb] Rant: B vs TLS, anisou, and PDB headers
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2008-03-29

Subject: Rant: B vs TLS, anisou, and PDB headers
From: Robbie Joosten rjoosten {- at -} CMBI {- dot -} RU {- dot -} NL
Date: 2008-03-29

ANISOU records imply that individual anisotropic B-factors were refined.
This will cause problems when you try to redo the final refinement: you add
loads of parameters all of a sudden. Using ANISOU records may give you more
reliable information about the B-factors, but not about the refinement.

Cheers,
Robbie Joosten

From: "Winn, MD (Martyn)"
Sent: Saturday, March 29, 2008 20:57
To:
Subject: Re: [ccp4bb] [phenixbb] Rant: B vs TLS, anisou, and PDB headers

>> 2) All you need to reproduce the R-factors are the ATOM records and
>> structure factor formula (and not ATOM records, PDB header with TLS
>> records that sometimes may be lost or manipulated and specific
>> converting programs to add TLS contribution). Also note, that not all
>> programs extract TLS information from PDB header to compute R-factors,
>> but ALL programs can read ATOM records.
>
> As you have stated this, it is not true. The big plus with TLS is that it
> models anisotropic displacements, which are not described in ATOM lines.
> You would need to include the (derived) ANISOU lines to reproduce
> R-factors. I bring this up again, because I feel undue respect is given to
> the total B factor (I have heard it called the "true" B factor - I have no
> idea what kind of truth that is!).
>
> Anyway, these are all different representations of the same thing, and
> should work equally well so long as you know which you are using. The
> scariest thing from the last thread was that our attempt to document it
> with a REMARK 3 line is being stripped by the RCSB.
>
> Cheers
> Martyn
>

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

Next message:
Subject: Re: [phenixbb] Rant: B vs TLS, anisou, and PDB headers
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2008-03-29