[gmx-users] The most probable secondary structure

[Justin A. Lemkul]

afsaneh maleki wrote:
> Hi,
> 
> how do i obtain the most probable secondary structure for each residue 
> to analyze the detailed conformation of the peptide?
> i used do_dssp then converted  *.eps to *.ps then obtained secondary 
> structure.
> 

You could write a script to parse through the output .xpm file, matching the 
incidence of the various secondary structure components per residue.  To get a 
more global perspective, simply collect statistics (i.e., g_analyze) from 
scount.xvg, but you won't be able to get a per-residue analysis this way.

-Justin

> highly appreciate!!
> 
> Afsaneh Maleki
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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