PROCHECK-NMR - Sample plots

1. Ramachandran plot

Description

The Ramachandran plot shows the phi-psi torsion angles for all residues in the ensemble (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.

The numbers within each data point correspond to the model number from which that point comes.

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

• A separate plot for each model in the ensemble (see the Options below).
• Separate plots for just the Gly & Pro residues.
• Separate plots for each of the 20 different amino acid types (available as an option in the Gly & Pro Ramachandran plots).
• Separate plots for each residue in the sequence.

Options

The main options for the Ramachandran plot are:-

• A separate Ramachandran plot can be generated for each of the models in the ensemble.
• 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 size of the data points, and whether the model-numbers are written inside them, can be varied.
• The plot can be in colour or black-and-white.

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

PROCHECK-NMR - Sample plots