1GMX-XPM2PS(1) GROMACS GMX-XPM2PS(1)
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6 gmx-xpm2ps - Convert XPM (XPixelMap) matrices to postscript or XPM
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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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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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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
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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
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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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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 2022, GROMACS development team
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1482022.3 Sep 02, 2022 GMX-XPM2PS(1)