Re: secondary structure analysis

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Jan 11 2013 - 03:34:55 CST

After installing the sscache script (so that the secondary structure is
update each frame) it is really easy to read:

#selection with one atom per residue
set sel [atomselect top "protein and name CA"]

# read the structure
$sel get structure
#->C C C C T T ....

Now you just have to loop through all frames.

Best regards,
Ajasja

On 11 January 2013 09:57, Nicholas M Glykos <glykos_at_mbg.duth.gr> wrote:

>
>
> > I know that stride computes this data, but I'm not sure where its
> > stored, or how to access it in a script.
>
> Recent versions of carma can produce a file containing secondary structure
> assignments from stride (you'll need an executable named 'stride' in the
> path (and a linux machine)). The file will look like this (one line per
> frame, one char per residue) :
>
> GGGGGGGGGHTT TTTTTTTTTTTTT
> TTGGGGGGGGGTTT TTTTTTTTTTGGG
> TTGGGTTTGGGTTT TTTTTTTGGG
> TTTGGGGGGGGGTTT TTTTTTTGGG
> TTGGGGGGGGGGTTTT TTTTTTTGGG
> GGGGG GGGGTTTT TTTTTTTGGG
> ...............
>
>
>
>
> --
>
>
> Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
>
>

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