Re: [AMBER] secondary structure plotting

From: Brendan Duggan <>
Date: Fri, 24 Jun 2011 10:51:13 -0400

If you want to plot the secondary structure averages over your entire
trajectory you can use the ".sum" file generated by the ptraj
secstruct command. Here you can plot the first column (residue
number) on the x axis against each of the other columns in turn.

If you want to monitor changes in secondary structure over the course
of your trajectory you can modify the file output by secstruc by
converting the labels for the secondary structure (GHIbBT) to numbers
(123456 for example). You can then assign a color to each number and
plot the appropriate color at the x,y co-ordinate defined by the
residue number and the time point. I use gnuplot to make these types
of plots.

Hope this helps


On Thu, Jun 23, 2011 at 4:45 PM, Jagur Lambix <> wrote:
> Dear Amber Users,
> I wanted to plot the secondary structure of the protein of interest.
> I have calculated it using the secstruct command in ptraj.
> However, I need some help how to plot the output of secstruct in order to show
> as a graphical presentation.
> can anyone help me, how to do that ? Does DSSP will help in that part ? Is there
> any other tool which can plot the secstruct output  ?
> Any suggestion is highly appreciated.
> Jagur
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Received on Fri Jun 24 2011 - 08:00:04 PDT
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