ramaStrip
Perform Ramachandran analysis on each specified residue.
Print contours levels containing 98% and 99.8% of all high-resolution structure. For each structure specified, plots a blue point if the associated phi/psi value lies inside the 99.8% contour, and a red point otherwise. For each structure, also print out all violated phi/psi values on stdout. For a description of the structure database and generation of the density surface, please see G.A. Bermejo, G.M. Clore, and C.D. Schwieters, Protein Science 21, 1824-1836 (2012).
Usage: ramaStrip [options] <pdb file1> [<pdb file2> ...]
where option is one or more of:
-psf <file name> - specify psf file- necessary if nonstandard residues
are present.
-selection <sel string> - XPLOR atom selection string specifying which
residues to display information about.
-model <model number> - Model number to use for the comparison
structure file[s]. The default behavior is
to compare to all models.
-noplot - do not make a plot- only make a list of violations.
-rows <num> - specify the number of rows in the output figure.
-columns <num> - specify the number of columns in the output figure.
-wintitle <text> - window title (for interactive display). If not
set the title will be set to the first coordinate
file name.
-axesNumbers - on plot, print the values of phi and psi along the
axes.
Interleaved in the PDB file list can be entries with the form color:colorName. If these are specified, the points are colored by the most recently preceeding color, instead of its violation status.