Re: [AMBER] cpptraj hist 3D

From: Jason Swails <>
Date: Thu, 6 Nov 2014 14:36:39 -0500

> On Nov 6, 2014, at 9:38 AM, andrea spitaleri <> wrote:
> In addition, you may try python with matplotlib/scipy:

matplotlib does not make plotting 3-D scalar data (like histograms) easy -- in fact, I don’t think it is possible (it can do surface plots, but only of functions of 2 variables; it cannot do surface contours of 3-dimensional functions). numpy can certainly do the histogramming, but the OP is already doing that with cpptraj.

I stumbled upon the Mayavi2 project which looks like it can do this, though. <>

I’ve never tried it myself, but they have both a GUI interface as well as a Python-scriptable API so you can use it like matplotlib. In any case it appears to be an open source alternative to the functionality in Mathematica and Matlab I described earlier.

Of course, you can always follow Dan’s advice and see if VMD can do the trick (although I don’t know if you can plot volumetric data without first loading a “molecule”, in which case that approach may be challenging).

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 06 2014 - 12:00:02 PST
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