Re: [AMBER] Plotting Issue

From: Jason Swails <>
Date: Thu, 16 Oct 2014 10:55:18 -0400

On Oct 16, 2014, at 10:26 AM, Soumendranath Bhakat <> wrote:

> Dear All;
> It is not a technical problem related to AMBER but I think some of you
> might suggest some interesting approach.
> We obtained distance between some particular residues as well as dihedral
> angle among some specified residues over a time scale of 50ns.
> I am just interested is there any way to plot distance and dihedral angle
> as a function of time with a 3D surface map or contour map approach (Say
> for example X axis=Time, Y= distance; Z= dihedral).

What you are trying to plot here is 4-dimensional. You have two options to do this:

You can use a movie (or animated gif) in which each frame is a surface plot of distance vs. dihedral at a particular time, so that time _is_ the time axis.

You can plot a contour (basically, all points in which the value of the function is a particular value). This is effectively how wavefunctions -- which are functions of x, y, and z -- are plotted. The surface is usually the surface that encloses 90% of the electron density (maybe more?) -- but it is a projection of the 4-dimensional surface into a 3-dimensional plot.

Or you can do a parametric plot.

I would use either matplotlib or gnuplot to do this.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 16 2014 - 08:00:02 PDT
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