[cmview-devel] contact map comparison using cmview

[Henning Stehr]

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.

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
>
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