Re: [PyMOL] Calculating % secondary structure

[Tsjerk W. <ts...@gm...>]

Hi Prija,

You can do it with a bit of Python

ss = [ i.ss for i in cmd.get_model("n. ca").atom ]
print "Helix content: %5.2f%%" % (100.0*ss.count("H")/len(ss))
print "Sheet content: %5.2f%%" % (100.0*ss.count("S")/len(ss))

The first line gets a list of the secondary structure flags of the
selection "n. ca".

Hope it helps,

Tsjerk

On Wed, Jul 7, 2010 at 8:44 AM, Prija Ponnan <pri...@gm...> wrote:
> Hello
> Can we calculate percentage secondary structural element using Pymol or
> please suggest me some other program for this purpose
> Prija
>
> --
> Prija Ponnan
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands