[gmx-users] SS from xpm file

[Mu Yuguang (Dr)]

Or you can write simple perl or awk program to read and calculate.

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
Sent: Monday, October 24, 2005 11:17 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SS from xpm file

On Mon, 2005-10-24 at 17:01 +0200, Nguyen Hoang Phuong wrote:
> Dear All,
> 
> after performing do_dssp, I got the file like ss.xpm which looks like
> 
> "SSSSSSSSSSSS~~~S~~~~~SSSSSSSSSSSS~STSSSSSSSTTTTTSTST~~~~S~~~S~~",
> "SSSSSSSSSSSSS~~SSSSSSSSSSSSSSSSSSSSTSSSSSSSTTTTTSTSTSSSSSSSSSSS",
> 
> each line contains the information about secondary structures of one
> residue. I would like to compute the percentages of the structures S,
T
> etc. for each residue. To this end I have to count how many letters S,
T
> of each line. Do you know how to performing this counting?
> 
> Many thanks in advance,
look in the xvg file that is produced as well.

> 
> Phuong
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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