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CCP4BB  March 2008

CCP4BB March 2008

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Subject:

Re: Rant: B vs TLS, anisou, and PDB headers

From:

Martyn Winn <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Mon, 31 Mar 2008 18:29:43 +0100

Content-Type:

text/plain

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text/plain (82 lines)

True enough. My comment was in the context of whether it is better to
deposit ANISOU lines as a representation of the anisotropy.

The default for BRES in TLSANL is indeed false. This was originally done
so as not to break the pre-existing RESTRAIN usage. This is taken care
of in the GUI, and for those using the command line, it is in the doc
and in the examples.

Cheers
Martyn

On Mon, 2008-03-31 at 17:34 +0100, Ian J. Tickle wrote:
> <[log in to unmask]>
>                A<7D3BC3901B4543D1A590B580971B9239@neuromancer>
>     <[log in to unmask]>
> From: "Ian Tickle" <[log in to unmask]>
> To: "Winn, MD (Martyn)" <[log in to unmask]>, <[log in to unmask]>
> Return-Path: [log in to unmask]
> X-OriginalArrivalTime: 31 Mar 2008 16:34:19.0370 (UTC)
>     FILETIME=[1165ACA0:01C8934D]
> 
> 
> > -----Original Message-----
> > From: [log in to unmask] 
> > [mailto:[log in to unmask]] On Behalf Of Winn, MD (Martyn)
> > Sent: 29 March 2008 20:56
> > To: Robbie Joosten; [log in to unmask]
> > Subject: RE: [ccp4bb] Rant: B vs TLS, anisou, and PDB headers
> > 
> > I believe the simplest and most honest thing to deposit are 
> > the parameters of your model,
> > viz the TLS parameters and the residual B factors. 
> > Derived quantities should be calculated as and when you need them.
> > 
> > m
> 
> What the parameters of the model are depends on how you calculate the
> structure factors.  I could equally well define the total Uaniso that
> goes into the SF calculation as:
> 
> 	Uaniso_from_TLS - diagonal_U_from_trace + diagonal_U_from_Biso
> 
> in which case the parameters are the TLS parameters and the full Biso's.
> In fact this is precisely what the Restrain program, which originally
> implemented TLS for PX refinement, did.  I never did understand the
> rationale to change this, because it seemed to go against the spirit of
> the ATOM/ANISOU records, where the Biso column contains the full Biso
> regardless of whether or not an ANISOU record is present.  Also I see
> that the TLSANL program, which was originally developed for use with
> Restrain, has the option BRESID to select residual or full Biso's in the
> PDB file, but the default is apparently (if we are to believe the
> documentation!) BRESID = false, i.e. assume full Biso's.  This surely is
> another source of potential confusion.
> 
> I think the onus is on program developers to maintain compatibility with
> pre-existing software (that was always something we were always
> cognisant of when we were developing Restrain), unless of course there
> are cogent reasons not to, but in this case I don't see compelling
> reasons to be incompatible.  I think you deviate from compatibility at
> your peril!
> 
> Cheers
> 
> -- Ian
> 
> 
> Disclaimer
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-- 
***********************************************************************
*                                                                     *
*               Dr. Martyn Winn                                       *
*                                                                     *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455    E-mail: [log in to unmask]                 *
*   Fax: +44 1925 603825    Skype name: martyn.winn                   * 
*             URL: http://www.ccp4.ac.uk/martyn/                      *
***********************************************************************

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