PROCHECK sample plots

Plot 1. Ramachandran plot

Description

The Ramachandran plot shows the phi-psi torsion angles for all residues in the structure (except those at the chain termini). Glycine residues are separately identified by triangles as these are not restricted to the regions of the plot appropriate to the other sidechain types.

The colouring/shading on the plot represents the different regions described in Morris et al. (1992): the darkest areas (here shown in red) correspond to the "core" regions representing the most favourable combinations of phi-psi values.

Ideally, one would hope to have over 90% of the residues in these "core" regions. The percentage of residues in the "core" regions is one of the better guides to stereochemical quality.

Note that additional Ramachandran plots can also be generated, as follows:-

• Separate plots for each of the 20 different amino acid types (see Plot 2. Ramachandran plots by residue type).
• Separate plots for just the Gly & Pro residues (available as an option in Plot 2. Ramachandran plots by residue type).

Options

The main options for the Ramachandran plot are:-

• Labelling of residues in disallowed regions can be switched off, or alternatively can be extended into the other regions.
• Shading/colouring of the different regions can be switched off.
• The plot can be in colour or black-and-white.
• A "publication version" of the plot (without the outer border and statistics) can be generated.

These options can be altered by editing the parameter file, procheck.prm, as described here.

PROCHECK sample plots