Ramachandran Plot

The Ramachandran plot function in the Model Panel plots the distribution of amino acid backbone conformations in peptide and protein structures. It is also implemented as the command ramachandran. See also: RR Distance Maps, Rotamers, Structure Measurements, ksdssp

Each amino acid residue is shown as a dot in a graph of φ vs. ψ, more commonly known as a Ramachandran plot or Ramachandran map. Residues are shown as blue dots, or when selected, as red dots. Conversely, clicking a single dot on the plot will select the corresponding residue in the structure.

Probability contours based on a reference set of high-resolution proteins can be shown on the plot as green lines. The reference set and resulting φ,ψ distributions are described in:

Structure validation by Cα geometry: φ,ψ and Cβ deviation. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Proteins. 2003 Feb 15;50(3):437-50

Probability contours can be displayed for different subsets of the amino acid residues in the reference proteins, as indicated next to Show region for:

None - no probability contours
Alanine (no repet sec struct) - alanine residues not in helix or sheet
General case (no repet sec struct) - residues not in helix or sheet
General case (not Gly, Pro or pre-Pro) - residues except for glycine, proline, and those immediately preceding prolines in sequence
Glycine (sym) - glycine residues, probabilities symmetrized
Glycine (sym, no repet sec struct) - glycine residues not in helix or sheet, probabilities symmetrized
Proline - proline residues
pre-Proline (not Gly or Pro) - residues immediately preceding prolines in sequence, except for glycine and proline

When the plot has mouse focus, the X and Y coordinates (in this case, φ and ψ values) of the cursor location on the graph are reported on the lower right. Below the plot are standard navigation icons provided by matplotlib.

Assign Residue Probabilities assigns an attribute named ramaProb to the amino acid residues, with values taken from the appropriate dataset for each residue (Proline for prolines, etc.), and opens the Render/Select by Attribute tool.

Close removes the Ramachandran plot. Help opens this manual page in a browser window.

Whether or not a Ramachandran plot is shown, phi (φ) and psi (ψ) are automatically assigned as residue attributes, and as such can be viewed/changed in the Selection Inspector or changed with setattr.

UCSF Computer Graphics Laboratory / September 2014