Re: [ccp4bb]: rmsd calculation

["David R. Cooper" <drc2n@unix.mail.virginia.edu>]

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Another method would be to use lsqman (Upsalla Software Factory).  The
RMsd_calc command calculates the rmsd for the specified domain using
your current alignment.
http://xray.bmc.uu.se/usf/lsqman_man.html#S59

Good luck,
David

___________________________________________
David Cooper, Ph.D.
University of Virginia
Molecular Physiology and Biological Physics
PO BOX 800736
Charlottesville, VA 22908-0736
(434) 982 - 3151


On Fri, 11 Apr 2003, cheom-gil cheong wrote:

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>
>
> Dear all :
>
> I have a probably trivial question.
> I have two structures where one is apo and the other bound the inhibitor.
> This protein is composed of three domains. I superimposed these two
> structures using whole protein and I know rmsd of whole protein. I want to
> calculate rmsd of only one domain without fitting this domain further
> because the two structures were superimposed already. Does anyone know how
> to calculate rmsd with already-fitted coordinates?
>
> Many thanks in advance.
>
>
> Cheomgil Cheong, Ph.D.
> Research Associate
> Department of Molecular Biology
> The Scripps Research Institute
> cheomgilcheong@hotmail.com
> cheong@scripps.edu
>
>
>
>
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