Re: [AMBER] significance of 3-10 helixes in Secstruct

From: Daniel Roe <>
Date: Sun, 15 Sep 2013 11:28:11 -0600


On Sat, Sep 14, 2013 at 3:51 PM, Chinthaka Ratnaweera <> wrote:
> 1. I am not very much aware about the 3-10 helixes. I understand these are
> similar to alpha helixes but have 3 residues per turn while alpha helix has
> 3.66 res per turn. But are these 3-10 helixes are experimentally
> significant? I am trying to interpret peaks for alpha helixes in CD
> spectra.

I'm not sure what you mean by "experimentally significant". The 3-10
helix is a valid secondary structure element; whether or not it
belongs in your particular system depends of course on what your
system is and what experimental evidence is available. I think you can
differentiate between alpha and 3-10 helices in certain systems using
VCD spectra.

> 2.I am using 'secstruct' in ptraj to generate secondary structure
> information. There is a way to visualize these plots in 2D in cpptraj with
> gnuplot. ( by gnu extension). But this can't be done in ptraj. Is there any
> script available to do this.

You could write your own script to convert the output from ptraj
'secstruct' so it is viewable in gnuplot, but why not save yourself
the trouble and just use cpptraj?


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sun Sep 15 2013 - 10:30:02 PDT
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