VMD-L Mailing List

From: Suman Chakrabarty (suman_at_sscu.iisc.ernet.in)
Date: Thu Feb 19 2009 - 12:27:25 CST

I shall be interested to know if you (and others) have found any
solution to this. I don't have a protein system though. I have a
simple linear polymer chain, which can have helical segments. I would
like to quantify the helical content in the chain.

Which would be right way to proceed here? Thanks for any help.

Regards,
Suman.

On Fri, Jan 16, 2009 at 12:39 AM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
> Hi, All:
>
> Is there a way to score a peptide chain according to its helicity, say to
> define a function f(h), and f(h) = 1 for perfect alpha helix, and f(h) = 0
> for random coil?
>
> I probably can hack the STRIDE code and get a start on this, but still, I
> want to hear your ideas. ;-)
>
> Any suggestion is appreciated.
>
> Thanks a lot.
>
> Bin