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RNAstructure Command Line Help
EnergyPlot

EnergyPlot is used to create a folding free energy plot generated after determining the structure of a strand or strands of nucleic acids.

USAGE: EnergyPlot <save file> <ps file> [options]

Required parameters:

<save file> The name of a binary folding save file containing free energy data from a previous folding calculation. These folding free energy save files usually end in ".sav".
<output file> The name of a file to which output will be written.
Depending on the options selected, this may be one of the following file types.
1) A Postscript image file.
2) An SVG image file.
3) A plain text file.

Options that do not require added values:

-h, -H, --help Display the usage details message.
--svg Specify that the output file should be an SVG image file, rather than a Postscript image file.
-t, -T, --text Write dot plot as a text file, rather than a Postscript image file.

Options that require added values:

-e, -E, --entries Specify the number of categories in the plot legend.
Default is 5 entries.
-max, -MAX, --maximum Specify the maximum value in the plot in kcal/mol.
Default is the largest valid value in the plot.
-min, -MIN, --minimum Specify the minimum value in the plot in kcal/mol.
Default is the smallest valid value in the plot.

References:

  1. Reuter, J.S. and Mathews, D.H.
    "RNAstructure: software for RNA secondary structure prediction and analysis."
    BMC Bioinformatics, 11:129. (2010).
  2. Zuker, M.
    "On finding all suboptimal foldings of an RNA molecule."
    Science, 244:48-52. (1989).