plotDihedral: plot dihedral angles

Command Line Flags

-a

Plot all dihedrals.

-b degrees

Normally, plotDihedral plots a single line for each dihedral angle sample. Specifying the -b flag makes it plot distribution as degrees size bins rather than individual lines. The default bin size is zero, which is the same as using individual lines.

-c columns

Display columns columns of plots per page. Note that columns is relative to the portrait page, regardless of whether the plots are rotated. The default number of columns is two.

-e

Generate Encapsulated PostScript. It is the responsibility of the user to make sure that only one page of output is generated.

-i

Interactive mode. Normally, when dihedrals have been selected using either the -a or -s flag, plotDihedral will plot the selected dihedrals without displaying the dihedral selection panel. Specifying the -i flag will make it always show the panel. Any pre-selected dihedral will be automatically selected in the panel as well.

-o output-file

Send PostScript output to output-file. Without this flag, plotDihedral sends PostScript to standard output.

-r rows

Display rows rows of plots per page. Note that rows is relative to the portrait page, regardless of whether the plots are rotated. The default number of rows is four.

-s dihedral-number

If the -a flag is not specified, select the dihedral-numberth dihedral for plotting; otherwise, deselect the dihedral-numberth dihedral for plotting. dihedral-number is the zero-based index of dihedrals found in the CARNAL output file after any type filtering specified by the -t flag. The -s flag is only for brave souls; others should use the selection panel in interactive mode (see the -i flag).

-t type

Use only dihedrals of type type from the CARNAL output file. Currently, the supported values for type are phi, psi, omega, and any. Only the type specified by the last -t flag is used. The default type is any.

-v

Print informational messages, including CARNAL output not preceded by `>', number of atoms, and number of dihedrals.

-A angle

Specify the angle (in degrees) at the bottom of a Cartesian plot. The default value is -180, which places zero degrees in the middle of the plot.

-D color

Specify the color of the distribution plot. Only the data portion is shown in color, i.e., the border will still be black. color is specified in RGB and must be in the format (r, g, b); the parentheses and commas are required elements and r, g and b must be between 0 and 1 inclusive. This option will probably be replaced by a more general color specification scheme.

-I format

Select input format. Currently, the only supported format (and hence the default) is carnal, for CARNAL dihedral analysis output. The two input-files required for carnal format are the CARNAL output file and table file.

-O format

Select output format. Currently, the supported formats are radial (default) and cartesian. See below for description of generated plots.

-T color

Specify the color of the time plot. Only the data portion is shown in color, i.e., the border will still be black. color is specified in RGB and must be in the format (r, g, b); the parentheses and commas are required elements and r, g and b must be between 0 and 1 inclusive. This option will probably be replaced by a more general color specification scheme.

input-files

List of input files to process. Required and permissible input files depend on the input format. See -I.

Description

Get Dihedral List

Read the output and table files from CARNAL to get a list of dihedral angle specifications and their values during a trajectory.

Filter Dihedral List

If the -t flag is specified, the dihedral list is filtered to select only those of the correct type.

Select Dihedrals

If no dihedrals are selected by the -a or -s, or if the -i flag is specified, plotDihedral displays a panel from which the user can select dihedrals of interest, as well as change the page layout parameters such as the number of columns and rows of plots per page, and distribution plot bin size.

Plot Selected Dihedrals

Plots of selected dihedral angles are generated in PostScript. If the -e flag is specified, the output is suitable for incorporation into other programs such as FrameMaker and Diagram.

Plot Layout

name: atom1 - atom2 = atom3 - atom4 (average / sigma)

residue-number:atom-number residue-type atom-name

Both the time and distribution plots are either radial or Cartesian plots. The radial time plot proceeds from the center to the perimeter of the circle, drawing lines between consecutive angle samples. The radial distribution plot have one of two appearances. If the distribution plot bin size is zero, a line is drawn from the center to the perimeter for each angle sample. If the bin size is non-zero, the circle is divided into pie slices that subtend the bin size (e.g., if the bin size is five degrees, then the circle is divided into seventy-two pie slices). For each pie slice, the number of samples falling in the slice determines the gray level of the pie slice. A slice with zero samples is white; a slice with more than half the total sample is black; all other slices will be a shade of gray proportional to the number of samples they contain. Any slice that contains at least one sample is guaranteed to be a visible shade of gray, i.e., it will not be so light gray as to be indistinguishable from white.

The Cartesian plots are rectangular instead of circular. For the Cartesian time plot, the y-axis represents the dihedral angle, with zero in the middle and 180 and -180 at the top and bottom respectively (this may be changed using the -A option); the x-axis represents time and proceeds from left to right. For the Cartesian distribution plot, the y-axis again represents the dihedral angle. If the distribution plot bin size is zero, horizontal lines spanning the plot are drawn for each angle sample. If the bin size is non-zero, the y-axis is divided into slices that correspond to the bin size. For each bin with one or more samples, a rectangle whose width is proportional to the number of samples in the bin is drawn. A rectangle that horizontally spans the plot represents a bin that contains 50% or more of the samples.

See Also

plotDihedral extension mechanisms.