Chimera Commands Index

ramachandran [ assign ]  atom-spec

The ramachandran command shows the distribution of peptide φ,ψ angles (a Ramachandran plot) for each specified model that contains protein. It is the command-line implementation of the Ramachandran plot function in the Model Panel. A separate plot will be generated for each protein-containing model with any atom in atom-spec, and the plot for a model will contain all of its peptide φ,ψ angles regardless of which atoms were specified.

The assign keyword indicates assigning an attribute named ramaProb to the amino acid residues, with values taken from the appropriate dataset for each residue (Proline for prolines, etc.).

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. See also: angle, rotation, swapaa