[cmview-devel] contact map comparison using cmview

Sikander Hayat sikander.hayat at scilifelab.se
Thu Dec 27 03:47:29 EST 2012


Hi Henning,

thanks for the replies.

On Mon, Dec 24, 2012 at 4:25 PM, Henning Stehr <stehr at molgen.mpg.de> wrote:

> Hi Sikander,
>
> to compare contact maps, you can load one in Casp RR format, then load
> the second one from the Compare menu. In the File->Info dialog you can
> see the overlap counts.
>
I did that, but is it possible to have a commandline version for it? i need
to do it for a large dataset and its not possible to do it one by one. i
dont need to visualize it, just need to get a measure of similarity between
maps.

>
> Now for secondary structure, I'm not sure what exactly you intend to
> do. If you have predicted secondary structure states for each residue,
> these can't be used in the contact map comparison unless you somehow
> translate them into contacts. For helices one may still assume some
> idealised geometry but for beta sheets you will need to know something
> about the overall topology to place them.
>
> Hope that helps.
>
> Henning
>
> On Sat, Dec 22, 2012 at 9:35 AM, Sikander Hayat
> <sikander.hayat at scilifelab.se> wrote:
> > Dear cmview team,
> >
> > my name is Sikander Hayat. I am a postdoc with Arne Elofsson at Stockholm
> > University.
> >
> > I want to use your software cmview to compare two contact maps generated
> > using predictions. I dont have a structure for them.... basically i want
> to
> > input two contact maps in casp format and their psipred predicted
> secondary
> > structure... and get a measurement of contact map similarity.
> >
> > can you please tell me how i can do that with your software..
> >
> > best wishes,
> > Sikander
> >
> > --
> > -Sikander Hayat
> > http://www.nada.kth.se/~shayat/
> >
> > Post-doc Researcher with Prof. Arne Elofsson
> > Stockholm University and Scilifelab Stockholm
> > Sweden
> >
> > _______________________________________________
> > cmview-devel mailing list
> > cmview-devel at bioinformatics.org
> > http://www.bioinformatics.org/mailman/listinfo/cmview-devel
> >
>



-- 
-Sikander Hayat
http://www.nada.kth.se/~shayat/

Post-doc Researcher with Prof. Arne Elofsson
Stockholm University and Scilifelab Stockholm
Sweden
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