The Ramachandran Plot popup provides one of the most important structure validation tools used in protein structure determination. The plot shows the combinations of the phi and psi backbone angles in a given protein structure as dots, which are plotted on top of a reference distribution map that contains the regions where the phi/psi combinations are found in good quality reference structures. The Ramachandran Plot thus provides an immediate indication of which residues are in abnormal regions. The plot can be customised by the user, and can be shown for all residues, residue types, or individual residues, each with a residue specific reference plot.

The Charts: Ramachandran Plot popup.

MolSystem

Specifies the molecular system from which structures are selected for Ramachandran plot generation.

Structure

Specifies the structure for which the Ramachandran plot is displayed.

Model

Specifies the model within the structure ensemble for which the Ramachandran plot is displayed.

Labels

Specifies which residues to label. By default only residues in disallowed regions are labelled. Other options are to label all or none of the residues.

Spot Size

Specifies teh size of the spots for each residue in the Ramachandran plot.

Colours

Specifies the colours of the spots in the plot.

CcpCode

Selects a residue type to be shown in the plot based on their CcpCode. This allows the user to display the results for a single amino acid type, on its residue specific Ramachandran reference distribution.

Residue

Select individual residues to be shown in the plot based on their CcpCode. This allows the user to display the results for a single amino acid type, on its residue specific Ramachandran reference distribution. The list of options is subdivided into sequence segments of 10 residues, preceded by the chain identifier, e.g.:

• • A 0 - 10

    • 2 His

    • 3 Thr

    • ...

    • 9 Ala

  • A 10 -20

    • ...

plot

This is the container for the actual Ramachandran plot. The plot is rastered into 10x10 degree bins, onto which the reference distribution for the selected residues is shown in a grey to red gradient. The more red a bin is, the higher the probablity is for a residue to be in found in this region of the Ramachandran plot.

The plot can be printed as a postscript file using the right mouse menu R:Print to file, which opens the Print canvas to file popup. The zoom can be reset with R:Reset Zoom.

Previous Residue

Displays the Ramachandran plot for the next residue in the sequence.

Next Residue

Displays the Ramachandran plot for the previous residue in the sequence.