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RAM, RAMACHANDRAN
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RAM, RAMACHANDRAN
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NAME
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RAM, RAMACHANDRAN - draw Ramachandran plot.
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SYNOPSIS
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RAM
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RAM SEL
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RAM OFF
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RAMACHANDRAN
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RAMACHANDRAN SEL
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RAMACHANDRAN OFF
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DESCRIPTION
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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.
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The main chain dihedral angles are defined as follows:
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(1) The phi angle is the angle of right-handed rotation around N-CA bond,
the value being zero if CA-C bond is cis to C-N bond. Range: from -180
to 180 degrees.
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(2) The psi angle is the angle of right-handed rotation around CA-C bond,
the value being zero if C-N bond is cis to N-CA bond. Range: from -180
to 180 degrees.
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(3) The omega angle is the angle of right-handed rotation about C-N bond,
the value being zero if CA-C bond of the preceding residue is cis to N-CA bond.
Most residues in a typical protein are involved in the formation of two
peptide bonds. The peptide bond formed by the residues I and I + 1 is assigned
to the residue I + 1. The same applies to the omega angle. For that reason no
omega angle is assigned to the first residue.
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Since version 1.2, garlic uses the following procedure to calculate the main
chain dihedral angles:
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(1) In the first attempt, the coordinates of the main chain atoms are used
to calculate the dihedral angles phi and psi. The phi angle will be missing
for the first residue in each chain. The psi angle will be missing for the
last residue in each chain.
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(2) In the second attempt, the missing phi angles will be calculated using the
coordinates of H (hydrogen) atoms, if available. The missing psi angles will
be calculated using the coordinates of O (oxygen) atoms.
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<IMG SRC="phipsi.gif">
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KEYWORDS
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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 off the 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 visible in
the 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:
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KEYWORD
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DESCRIPTION
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ram sel
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Draw Ramachandran plot for selected residues.
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ram off
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Return to default drawing mode (atomic structure).
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Instead using this command, you can hit the ESCAPE key.
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MOUSE USAGE
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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:
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<IMG SRC="ramacont.gif">
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EXAMPLE OF RAMACHANDRAN PLOT
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The example below show the Ramachandran plot for photosynthetic reaction center
from Rhodopseudomonas viridis.
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<IMG SRC="ramaplot.gif">
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EXAMPLES
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COMMAND
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DESCRIPTION
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ram
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Draw Ramachandran plot for all residues.
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ram off
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Return to default drawing mode (atomic structure).
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ram sel
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<TD ALIGN="left">
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Draw Ramachandran plot for selected residues.
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sel pro
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ram sel
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Select all prolines and draw Ramachandran
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plot for prolines.
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sel cis
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ram sel
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Select all residues in cis conformation and
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draw Ramachandran plot for them.
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sel bad
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ram sel
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Select bad residues (peptide unit not planar)
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and draw Ramachandran plot.
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sel tra
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ram sel
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Select all residues in trans conformation and
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draw Ramachandran plot.
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NOTES
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(1) Instead using the command RAMA OFF, the ESCAPE key may be pressed to
return to the main drawing mode.
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(2) G. N. Ramachandran devised in the late 1960's the steric constraints 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:
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<A HREF="http://xray.bmc.uu.se/~gerard/rama/ramarev.html">
http://xray.bmc.uu.se/~gerard/rama/ramarev.html
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RELATED COMMANDS
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SEL may be used to select a portion of protein structure, to reduce the
amount of data in Ramachandran plot.
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