Dear Filip,
as Roberto mentioned earlier, our program Escet, respectively the RAPIDO
web server - http://webapps.embl-hamburg.de/rapido/ - is taking
coordinate errors (as derived from DPI- or empirically scaled B-factors)
into account when judging the significance of structural invariance
(that is, in particular domain movement). As far as crystal structures
are concerned, you may want to give it a try ... otherwise I agree on
the suggestion to compare the "internal" rmsd of individually
superimposed domains to the overall rmsd of superimposed multi-domain
structures, or more specifically, to the concerted shift of a domain
relative to the other(s), so to estimate the resolution-independent
significance of movement.
Cheers,
Fabio
--
Dr. rer. nat. Fabio Dall'Antonia
European Molecular Biology Laboratory c/o DESY
Notkestraße 85, Bldg. 25a
D-22603 Hamburg
phone: +49 (0)40 89902-170
fax: +49 (0)40 89902-149
e-mail: fabio.dallanto...@embl-hamburg.de
On 11/22/11 1:00 AM, CCP4BB automatic digest system wrote:
Date: Mon, 21 Nov 2011 15:56:40 -0700 From: James Stroud
<xtald...@gmail.com> Subject: Re: Movements of domains On Nov 21,
2011, at 3:04 PM, Filip Van Petegem wrote:
> So the question is: how you can state that a particular movement was
'significantly large' compared to the resolution limit?
I can think of a different but related question. How significant is a
particular movement compared to a measured coordinate error? One way to measure
the coordinate error in this example is to least-squares superpose the two
instances of the domain in question and calculate the rmsd.
This makes the calculation of significance independent of the resolution of the
data set.
James
