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Re: [ccp4bb]: dyndom problem



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Hi,
You can consider to use DOMOV to detect the domain movement.
http://bioinfo1.mbfys.lu.se/cgi-bin/Domov/domov.cgi

or you could download TOP and FIT program and a unix script PSHIF
to do the same thing (and visualize the movement on display by O program)
 http://bioinfo1.mbfys.lu.se/TOP/pshif.html

pautsch wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
>
> Hi
>
> I would have liked to charakterize a  domain movement in 2 closely
> related proteins with DYNDOM.
> Following the scripts provided and fiddling with the parameters I always
> end up with thenfollowing message:
>
> >>>>>>
> ********************************************************
> WARNING NUMBER OF RESIDUES IN CHAINS IS DIFFERENT 303 300
>
> determining backbone atoms of first conformer
>
> determining backbone atoms of second conformer
>
> number of residues used for analysis:  300
>
> rmsd of whole protein best fit:    6.969 A
>
> number of clusters:   1
>
> number of clusters:   2
> found cluster for which all domains are less than minimum domain size
> so we stop
>
> NO DYNAMIC DOMAINS FOUND
> TRY ALTERING PARAMETER VALUES
>
> <<<<<
>
> I went on to try one of the default examples from the DynDom homepage
> (cAMP dep. Kinase) with the exactly the scripts provided and the
> respective pdb-files. But got the  same result:
>
> >>>>>
> :
> :
> number of clusters:   3
> found cluster for which all domains are less than minimum domain size
> so we stop
>
> NO DYNAMIC DOMAINS FOUND
> TRY ALTERING PARAMETER VALUES
>
> <<<
>
> Is this a bug or (more likely) did I miss something?
>
> Cheers
>
> Alex

--
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Guoguang Lu, PhD, Universitetslektor
Dept of Molecular Biophysics
Center for Chemistry and Chemical Engineering
Lund University
Box 124, SE-221 00 Lund, Sweden
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