1GMX-XPM2PS(1)                       GROMACS                      GMX-XPM2PS(1)
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NAME

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

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

18       gmx  xpm2ps  makes a beautiful color plot of an XPixelMap file.  Labels
19       and axis can be displayed, when they are supplied in the correct matrix
20       format.   Matrix data may be generated by programs such as gmx do_dssp,
21       gmx rms or gmx mdmat.
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23       Parameters are set in the .m2p file optionally supplied with -di.  Rea‐
24       sonable defaults are provided. Settings for the y-axis default to those
25       for the x-axis. Font names have a defaulting  hierarchy:  titlefont  ->
26       legendfont;  titlefont  ->  (xfont -> yfont -> ytickfont) -> xtickfont,
27       e.g. setting titlefont sets all fonts, setting xfont sets yfont, ytick‐
28       font and xtickfont.
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30       When  no  .m2p  file  is supplied, many settings are taken from command
31       line options. The most important option is -size, which sets  the  size
32       of the whole matrix in postscript units.  This option can be overridden
33       with the -bx and -by options (and the corresponding parameters  in  the
34       .m2p file), which set the size of a single matrix element.
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36       With  -f2  a second matrix file can be supplied. Both matrix files will
37       be read simultaneously and the upper left half of the first one (-f) is
38       plotted together with the lower right half of the second one (-f2). The
39       diagonal will contain values from the matrix file selected with  -diag.
40       Plotting of the diagonal values can be suppressed altogether by setting
41       -diag to none.  In this case, a new color map will be generated with  a
42       red  gradient  for  negative  numbers  and a blue for positive.  If the
43       color coding and legend labels of both matrices are identical, only one
44       legend  will  be  displayed,  else  two separate legends are displayed.
45       With -combine, an alternative operation can be selected to combine  the
46       matrices.  The output range is automatically set to the actual range of
47       the combined matrix. This can be overridden with -cmin and -cmax.
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49       -title can be set to none to suppress the title, or to ylabel  to  show
50       the title in the Y-label position (alongside the y-axis).
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52       With  the  -rainbow  option, dull grayscale matrices can be turned into
53       attractive color pictures.
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55       Merged or rainbowed matrices can be written to an XPixelMap  file  with
56       the -xpm option.
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OPTIONS

59       Options to specify input files:
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61       -f [<.xpm>] (root.xpm)
62              X PixMap compatible matrix file
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64       -f2 [<.xpm>] (root2.xpm) (Optional)
65              X PixMap compatible matrix file
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67       -di [<.m2p>] (ps.m2p) (Optional, Library)
68              Input file for mat2ps
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70       Options to specify output files:
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72       -do [<.m2p>] (out.m2p) (Optional)
73              Input file for mat2ps
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75       -o [<.eps>] (plot.eps) (Optional)
76              Encapsulated PostScript (tm) file
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78       -xpm [<.xpm>] (root.xpm) (Optional)
79              X PixMap compatible matrix file
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81       Other options:
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83       -[no]w (no)
84              View output .xvg, .xpm, .eps and .pdb files
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86       -[no]frame (yes)
87              Display frame, ticks, labels, title and legend
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89       -title <enum> (top)
90              Show title at: top, once, ylabel, none
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92       -[no]yonce (no)
93              Show y-label only once
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95       -legend <enum> (both)
96              Show legend: both, first, second, none
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98       -diag <enum> (first)
99              Diagonal: first, second, none
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101       -size <real> (400)
102              Horizontal size of the matrix in ps units
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104       -bx <real> (0)
105              Element  x-size,  overrides  -size  (also y-size when -by is not
106              set)
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108       -by <real> (0)
109              Element y-size
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111       -rainbow <enum> (no)
112              Rainbow colors, convert white to: no, blue, red
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114       -gradient <vector> (0 0 0)
115              Re-scale colormap to a smooth gradient  from  white  {1,1,1}  to
116              {r,g,b}
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118       -skip <int> (1)
119              only write out every nr-th row and column
120
121       -[no]zeroline (no)
122              insert line in .xpm matrix where axis label is zero
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124       -legoffset <int> (0)
125              Skip first N colors from .xpm file for the legend
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127       -combine <enum> (halves)
128              Combine two matrices: halves, add, sub, mult, div
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130       -cmin <real> (0)
131              Minimum for combination output
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133       -cmax <real> (0)
134              Maximum for combination output
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SEE ALSO

137       gmx(1)
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139       More     information    about    GROMACS    is    available    at    <‐
140       http://www.gromacs.org/>.
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143       2019, GROMACS development team
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1482019.2                           Apr 16, 2019                    GMX-XPM2PS(1)
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