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[ccp4bb]: dyndom problem (fwd)
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You could try reducing the minimum domain size with
the "domain" keyword. That's your immediate problem,
but may not be the fundamental problem.
Martyn
> 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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* *
* Dr. Martyn Winn *
* *
* Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND *
* Tel: +44 1925 603455 E-mail: m.d.winn@ccp4.ac.uk (personal) *
* Fax: +44 1925 603124 E-mail: ccp4@ccp4.ac.uk (CCP4 problems) *
* URL: http://www.dl.ac.uk/CCP/CCP4/martyn/martyn.html *
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