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Man Pages


Manual Reference Pages  -  GMX-XPM2PS (1)

NAME

gmx-xpm2ps - Convert XPM (XPixelMap) matrices to postscript or XPM

CONTENTS

Synopsis
Description
Options
See Also

SYNOPSIS

gmx xpm2ps [-f [<.xpm>]] [-f2 [<.xpm>]] [-di [<.m2p>]]
[-do [<.m2p>]] [-o [<.eps>]] [-xpm [<.xpm>]] [-nice <int>]
[-[no]w] [-[no]frame] [-title <enum>] [-[no]yonce]
[-legend <enum>] [-diag <enum>] [-size <real>]
[-bx <real>] [-by <real>] [-rainbow <enum>]
[-gradient <vector>] [-skip <int>] [-[no]zeroline]
[-legoffset <int>] [-combine <enum>] [-cmin <real>]
[-cmax <real>]

DESCRIPTION

gmx xpm2ps makes a beautiful color plot of an XPixelMap file. Labels and axis can be displayed, when they are supplied in the correct matrix format. Matrix data may be generated by programs such as gmx do_dssp, gmx rms or gmx mdmat.

Parameters are set in the .m2p file optionally supplied with -di. Reasonable defaults are provided. Settings for the y-axis default to those for the x-axis. Font names have a defaulting hierarchy: titlefont - legendfont; titlefont - (xfont - yfont - ytickfont) - xtickfont, e.g. setting titlefont sets all fonts, setting xfont sets yfont, ytickfont and xtickfont.

When no .m2p file is supplied, many settings are taken from command line options. The most important option is -size, which sets the size of the whole matrix in postscript units. This option can be overridden with the -bx and -by options (and the corresponding parameters in the .m2p file), which set the size of a single matrix element.

With -f2 a second matrix file can be supplied. Both matrix files will be read simultaneously and the upper left half of the first one (-f) is plotted together with the lower right half of the second one (-f2). The diagonal will contain values from the matrix file selected with -diag. Plotting of the diagonal values can be suppressed altogether by setting -diag to none. In this case, a new color map will be generated with a red gradient for negative numbers and a blue for positive. If the color coding and legend labels of both matrices are identical, only one legend will be displayed, else two separate legends are displayed. With -combine, an alternative operation can be selected to combine the matrices. The output range is automatically set to the actual range of the combined matrix. This can be overridden with -cmin and -cmax.

-title can be set to none to suppress the title, or to ylabel to show the title in the Y-label position (alongside the y-axis).

With the -rainbow option, dull grayscale matrices can be turned into attractive color pictures.

Merged or rainbowed matrices can be written to an XPixelMap file with the -xpm option.

OPTIONS

Options to specify input and output files:

-f [<.xpm>] (root.xpm) (Input)
X PixMap compatible matrix file

-f2 [<.xpm>] (root2.xpm) (Input, Optional)
X PixMap compatible matrix file

-di [<.m2p>] (ps.m2p) (Input, Optional, Library)
Input file for mat2ps

-do [<.m2p>] (out.m2p) (Output, Optional)
Input file for mat2ps

-o [<.eps>] (plot.eps) (Output, Optional)
Encapsulated PostScript (tm) file

-xpm [<.xpm>] (root.xpm) (Output, Optional)
X PixMap compatible matrix file

Other options:

-nice <int> (0)
Set the nicelevel

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files

-[no]frame (yes)
Display frame, ticks, labels, title and legend

-title <enum> (top)
Show title at: top, once, ylabel, none

-[no]yonce (no)
Show y-label only once

-legend <enum> (both)
Show legend: both, first, second, none

-diag <enum> (first)
Diagonal: first, second, none

-size <real> (400)
Horizontal size of the matrix in ps units

-bx <real> (0)
Element x-size, overrides -size (also y-size when -by is not set)

-by <real> (0)
Element y-size

-rainbow <enum> (no)
Rainbow colors, convert white to: no, blue, red

-gradient <vector> (0 0 0)
Re-scale colormap to a smooth gradient from white {1,1,1} to {r,g,b}

-skip <int> (1)
only write out every nr-th row and column

-[no]zeroline (no)
insert line in .xpm matrix where axis label is zero

-legoffset <int> (0)
Skip first N colors from .xpm file for the legend

-combine <enum> (halves)
Combine two matrices: halves, add, sub, mult, div

-cmin <real> (0)
Minimum for combination output

-cmax <real> (0)
Maximum for combination output

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.

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VERSION 5.0.6 GMX-XPM2PS (1)

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