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
[EMAIL PROTECTED]
GPG key ID: 38E9EB53
https://www.molevo.org/keys/38E9EB53.gpgkey
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