[gmx-users] The most probable secondary structure

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 19 13:15:04 CET 2010

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.


> highly appreciate!!
> Afsaneh Maleki


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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