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[gromacs/rigid-bodies.git] / man / man1 / xpm2ps.1

.TH xpm2ps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
xpm2ps - converts XPM matrices to encapsulated postscript (or XPM)

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3xpm2ps\fP
.BI "\-f" " root.xpm "
.BI "\-f2" " root2.xpm "
.BI "\-di" " ps.m2p "
.BI "\-do" " out.m2p "
.BI "\-o" " plot.eps "
.BI "\-xpm" " root.xpm "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-[no]w" ""
.BI "\-[no]frame" ""
.BI "\-title" " enum "
.BI "\-[no]yonce" ""
.BI "\-legend" " enum "
.BI "\-diag" " enum "
.BI "\-size" " real "
.BI "\-bx" " real "
.BI "\-by" " real "
.BI "\-rainbow" " enum "
.BI "\-gradient" " vector "
.BI "\-skip" " int "
.BI "\-[no]zeroline" ""
.BI "\-legoffset" " int "
.BI "\-combine" " enum "
.BI "\-cmin" " real "
.BI "\-cmax" " real "
.SH DESCRIPTION
\&\fB xpm2ps\fR 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 \fB do_dssp\fR, \fB g_rms\fR or
\&\fB g_mdmat\fR.


\&Parameters are set in the \fB .m2p\fR file optionally supplied with
\&\fB \-di\fR. Reasonable defaults are provided. Settings for the \fI y\fR\-axis
\&default to those for the \fI x\fR\-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 \fB .m2p\fR file is supplied, many settings are taken from
\&command line options. The most important option is \fB \-size\fR,
\&which sets the size of the whole matrix in postscript units.
\&This option can be overridden with the \fB \-bx\fR and \fB \-by\fR
\&options (and the corresponding parameters in the \fB .m2p\fR file),
\&which set the size of a single matrix element.


\&With \fB \-f2\fR a second matrix file can be supplied. Both matrix
\&files will be read simultaneously and the upper left half of the
\&first one (\fB \-f\fR) is plotted together with the lower right
\&half of the second one (\fB \-f2\fR). The diagonal will contain
\&values from the matrix file selected with \fB \-diag\fR.
\&Plotting of the diagonal values can be suppressed altogether by
\&setting \fB \-diag\fR to \fB none\fR.
\&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 \fB \-combine\fR, 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 \fB \-cmin\fR and \fB \-cmax\fR.


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


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


\&Merged or rainbowed matrices can be written to an XPixelMap file with
\&the \fB \-xpm\fR option.
.SH FILES
.BI "\-f" " root.xpm" 
.B Input
 X PixMap compatible matrix file 

.BI "\-f2" " root2.xpm" 
.B Input, Opt.
 X PixMap compatible matrix file 

.BI "\-di" " ps.m2p" 
.B Input, Opt., Lib.
 Input file for mat2ps 

.BI "\-do" " out.m2p" 
.B Output, Opt.
 Input file for mat2ps 

.BI "\-o" " plot.eps" 
.B Output, Opt.
 Encapsulated PostScript (tm) file 

.BI "\-xpm" " root.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-[no]frame"  "yes   "
 Display frame, ticks, labels, title and legend

.BI "\-title"  " enum" " top" 
 Show title at: \fB top\fR, \fB once\fR, \fB ylabel\fR or \fB none\fR

.BI "\-[no]yonce"  "no    "
 Show y\-label only once

.BI "\-legend"  " enum" " both" 
 Show legend: \fB both\fR, \fB first\fR, \fB second\fR or \fB none\fR

.BI "\-diag"  " enum" " first" 
 Diagonal: \fB first\fR, \fB second\fR or \fB none\fR

.BI "\-size"  " real" " 400   " 
 Horizontal size of the matrix in ps units

.BI "\-bx"  " real" " 0     " 
 Element x\-size, overrides \fB \-size\fR (also y\-size when \fB \-by\fR is not set)

.BI "\-by"  " real" " 0     " 
 Element y\-size

.BI "\-rainbow"  " enum" " no" 
 Rainbow colors, convert white to: \fB no\fR, \fB blue\fR or \fB red\fR

.BI "\-gradient"  " vector" " 0 0 0" 
 Re\-scale colormap to a smooth gradient from white {1,1,1} to {r,g,b}

.BI "\-skip"  " int" " 1" 
 only write out every nr\-th row and column

.BI "\-[no]zeroline"  "no    "
 insert line in \fB .xpm\fR matrix where axis label is zero

.BI "\-legoffset"  " int" " 0" 
 Skip first N colors from \fB .xpm\fR file for the legend

.BI "\-combine"  " enum" " halves" 
 Combine two matrices: \fB halves\fR, \fB add\fR, \fB sub\fR, \fB mult\fR or \fB div\fR

.BI "\-cmin"  " real" " 0     " 
 Minimum for combination output

.BI "\-cmax"  " real" " 0     " 
 Maximum for combination output

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.