On Oct 16, 2014, at 10:26 AM, Soumendranath Bhakat <bhakatsoumendranath.gmail.com> 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.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 16 2014 - 08:00:02 PDT
