Nicholas M. Glykos' group


Plot: a simple plotting program plot is a small, simple and straightforward plotting program for GNU/Linux and MacOSX (and even Windows 11 through winbash). plot may be useful to people that love working from within the unix shell, hate herding the mouse around, and need an extremely lightweight plotting program that can read standard input and can be used in unix pipelines.

plot can do simple x-y plots, can overlay two x-y plots, can draw histograms, can do scatter plots, and can draw contour or pseudo-color representations of your matrices (supporting bicubic interpolation for small matrices and plotting of both positive and negative contours).

Enough with that, let's get down to business: here is the tutorial with plenty of screenshots. Get the compressed archive plot-v.1.3.tar.gz (1.5 MBytes). The distribution includes source code, documentation and pre-compiled executables suitable for Linux and MacOS.

Spherical harmonics

Screenshot, 29 Kbytes This little program (in OpenGL) plots (and spins) the graph of the following equation :

and it allows you to change the values of the parameters (A,B,C,D,E,F,G,H) while observing the effects of your changes. Download the linux executable (don't forget to chmod it) or the source code (sph.c) which you can compile with something in the spirit of cc sph.c -lglut -lGLU -lGL -lXext -lX11 -lm

Fourier for hp48

Manual page for the program Fourier If you are a proud owner of a Hewlett Packard HP48 calculator, you may be interested in downloading the two short (system RPL) programs included in the file hp48.tar.gz (compressed tar archive). The first program allows you to perform two-dimensional forward and inverse geometric Fourier transforms (not FFT) and two-dimensional map plotting (see the manual page for more details). The second program will allow you (given a set of unit cell dimensions) to calculate the reciprocal unit cell dimensions and volume, and the Bragg spacing corresponding to a given reflection.

Pepinsky's machine

Screenshot Pepinsky's machine is a program aiming to help with the teaching of crystallographic Fourier transforms: Given a set of structure factor amplitudes for any centrosymmetric plane group, the program displays the amplitude-weighted reciprocal lattice plane and allows the user to interactively assign and modify the phases of the structure factors, while observing the effect of these changes on the corresponding electron density function (screenshot). See the documentation (1.1 MBytes) or the corresponding publication for more details.

Get the compressed archive pepinsky.tar.gz (3.1 MBytes). The distribution includes source code, documentation, example scripts, a couple of exercises and pre-compiled executables suitable for Irix, Linux, OSF and solaris. Get also this newer linux executable.

You can get Pepinsky's machine running smoothly on Windows 10 through the bash interface. Follow this guide, then type 'pepinsky' from the windows bash shell and you should see it.


Comparison between npo and mcps output mcps is a little program that will allow you to automatically plot a section from a CCP4 map file using both a grayscale (actually, dithered monochrome) representation and contour lines. This can be quite useful when the map contains significant fluctuations at high (or low) density, making it difficult to decide whether a feature is a peak or valley (see this graph for a comparison between the classical contour-line plot and the output from mcps in the case of a "difficult" map). You can also view an electronic reprint (html) of an article that appeared in the CCP4 Newsletter (March 2002).

Get the compressed archive mcps.tar.gz (812 KBytes). The distribution includes documentation (manual page, html) and pre-compiled executables suitable for Irix, Linux, OSF and solaris.