1. Introduction

These Operating Instructions describe how to run the LIGPLOT program (Wallace et al., 1995).

The program automatically generates schematic diagrams of interactions in proteins from the 3D coordinates alone. (Some examples are given here). It is particularly useful for comparing different structures, such as the interactions of different ligands with the same enzyme.

The inputs to LIGPLOT comprise:

the PDB file (Bernstein et al., 1977) holding the coordinates of the structure of interest,
a list of hydrogen-bonds and
a list of hydrophobic contacts within the structure.

The latter two lists can be automatically generated using the HBPLUS program which is supplied separately from LIGPLOT, and is described elsewhere (McDonald & Thornton, 1994). A parameter file, called ligplot.par can be edited to alter the parameters that control the appearance of the plot generated - eg colours, text sizes, etc (see section 5).

The outputs from LIGPLOT include:

the PostScript file showing the plotted schematic diagram and
various files that allow the diagram to be amended to the user's requirements (see section 6).

The LIGPLOT algorithm is described in detail in Wallace et al. (1995). In principle, it takes the 3D structure of the ligand and `unrolls' it about its rotatable bonds, flattening it out onto the 2D page. As it does so, it takes with it the hydrogen-bonded sidechains and sidechains involved in hydrophobic contacts, flattening those out too and placing them so that the overlap of atoms and the crossing of bonds in the final diagram is kept to a minumum.

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