From: Fabio Dall'Antonia
Date: 22 November 2011 09:36
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.
On 11/22/11 1:00 AM, CCP4BB automatic digest system wrote:
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
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