Re: [ccp4bb] superpose

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CCP4bb <-- 2007 <-- March 2007 <-- 12 March 2007

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Subject: superpose
From: "Juan Sanchez-Weatherby (UEA)" j {- dot -} sanchez-weatherby {- at -} UEA {- dot -} AC {- dot -} UK
Date: 2007-03-12

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From: James Whisstock James {- dot -} Whisstock {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU
Date: 2007-03-12

Subject: Re: superpose
From: "Douglas L {- dot -} Theobald" dtheobald {- at -} BRANDEIS {- dot -} EDU
Date: 2007-03-12

Hi Juan,

This doesn't directly apply to Superpose -- but THESEUS (which does
both conventional least-squares and maximum likelihood
superpositions) puts RMSD values by default in the B-factor column of
the PDB of the mean structure for a superposition. It is
undocumented, but via the THESEUS also will weight the superposition
by B-factor, using the B-factors as Bayesian priors for the
variances. It can do this two different ways, either (1) by assuming
that the B-factors are absolutely known values or (2) by assuming
that the B-factors for a structure are only known up to a scale
factor (use command line flags -b1 or -b2 respectively). For the
latter case, which is most realistic, THESEUS finds the maximum
likelihood value for the normalization factor for each structure.

http://www.theseus3d.org/

Cheers,

Douglas

On Mar 12, 2007, at 12:13 PM, Juan Sanchez-Weatherby (UEA) wrote:

> Dear all
> I have three questions that might have been answered before but I
> haven't been able to find them.
> 1) I was wondering whether anyone could tell me what does (in the
> Superpose output) "RMS B DISPLACEMENT" stand for?
> 2) If "B" is B-factor how meaningful is it if the haven't been
> normalised prior to the comparison?
>
> 3) Lastly I was wondering if there is a way of putting RMS
> deviation values in the B-factor column of a PDB file so it can
> coloured according to RMS instead of B-factor.

> Thank you very much
> Juan
> Juan Sanchez-Weatherby
> School of Biological Sciences
> University of East Anglia
> Norwich NR4 7TJ
> United Kingdom

^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`
Douglas L. Theobald
Department of Biochemistry
Brandeis University
Waltham, MA 02454-9110

dtheobald@brandeis.edu
GPG key ID: 38E9EB53
https://www.molevo.org/keys/38E9EB53.gpgkey

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CCP4bb <-- 2007 <-- March 2007 <-- 12 March 2007

Previous message:
Subject: superpose
From: "Juan Sanchez-Weatherby (UEA)" j {- dot -} sanchez-weatherby {- at -} UEA {- dot -} AC {- dot -} UK
Date: 2007-03-12

Next message:
Subject: Re: surface drawings
From: James Whisstock James {- dot -} Whisstock {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU
Date: 2007-03-12