RAM, RAMACHANDRAN

NAME
RAM, RAMACHANDRAN - draw Ramachandran plot.

SYNOPSIS
RAM
RAM SEL
RAM OFF
RAMACHANDRAN
RAMACHANDRAN SEL
RAMACHANDRAN OFF

DESCRIPTION
Draw Ramachandran plot (only for proteins). The main chain torsion angles, phi and psi, are used to prepare two-dimensional scatter plot. Residues for which both phi and psi angle may be calculated will be shown as small circles. The horizontal axis (abscisa) is used for phi values, while the vertical axis (ordinate) is used for psi values. Blue color is used for trans residues, magenta for cis residues and red for bad residues. Trans residues are drawn first, followed by cis residues. Bad residues are drawn last. A residue is treated as bad if peptide unit associated with this residue is not planar. Peptide unit is considered as non-planar if it is twisted for more than 20 degrees. Terminal residues will be missing, because at least one of dihedral angles is not defined for such residues.

Dihedral angles are defined as follows:

(1) The phi angle is the angle of right-handed rotation around N-CA bond, the value being zero if CA-C bond is trans to N-H bond. Range: from -180 to 180 degrees.

(2) The psi angle is the angle of right-handed rotation around CA-C bond, the value being zero if N-CA bond is trans to C-O bond. Range: from -180 to 180 degrees.



KEYWORDS
If used without any keyword, the command RAM will prepare the Ramachandran plot for protein structure(s) which are currently being handled ("caught"). Keyword OFF is used to switch Ramachandran plot, i.e. to return to the main drawing mode (atomic structure display). If keyword SEL (SELECTED) is used, only the residues which are currently selected will be included in Ramachandran plot. A residue is treated as selected if the first atom of this residue is selected. For proteins, this is usually N (nitrogen) atom. Here is the overview:

KEYWORD DESCRIPTION
ram sel Draw Ramachandran plot for selected residues.
ram off Return to default drawing mode (atomic structure).
Instead using this command, you can hit the ESCAPE key.

MOUSE USAGE
Pointing device (mouse) may be used to identify individual residues in Ramachandran plot. Just place the mouse pointer above the selected residue and the most important data for this residue will be shown in the output window. The output window will look like this:



EXAMPLE OF RAMACHANDRAN PLOT
The example below show the Ramachandran plot for one typical globular protein, consisting of 250 residues. Only the essential part of the main garlic window is shown.



EXAMPLES
COMMAND DESCRIPTION
ram Draw Ramachandran plot for all residues.
ram off Return to default drawing mode (atomic structure).
ram sel Draw Ramachandran plot for selected residues.
sel pro
ram sel 		Select all prolines and draw Ramachandran
plot for prolines.
sel cis
ram sel 		Select all residues in cis conformation and
draw Ramachandran plot for them.
sel bad
ram sel 		Select bad residues (peptide unit not planar)
and draw Ramachandran plot.
sel tra
ram sel 		Select all residues in trans conformation and
draw Ramachandran plot.

NOTES
(1) Instead using the command RAMA OFF, the ESCAPE key may be pressed to return to the main drawing mode.

(2) G. N. Ramachandran devised in the late 1960's the steric constrains for amino acid residues in proteins. As the number of high resolution structures is increasing, it appears evident that these old constrains are becoming obsolete. If you are interested in this problem, read this article:

alpha2.bmc.uu.se/~gerard/rama/rama.html

RELATED COMMANDS
SEL may be used to select a portion of protein structure, to reduce the amount of data in Ramachandran plot.