| ## RNAstructure Command Line Help draw | ### Contents ### Index
draw is used to draw secondary structures as Postscript images. These Postscript images can be drawn in a variety of ways, including annotated or circularized. Every individual structure is sized to fit on a single Postscript page. ### USAGE: draw <ct file> <ps file> [options] ### Required parameters:
<ct file> | The name of a CT file or Dot-Bracket file containing data for the structure to be drawn.
<output file> | The name of an image file to which output will be written. Usually, this is a Postscript image file, although the user can specify that it be an SVG image file instead. To specify SVG images, the \"--svg\" flag must be specified in conjunction with a structure number flag (see the flags below).
### Options that do not require added values:
-c, -C, --circle | Specify that the structure should be drawn with its backbone around a circle. Note that pseudoknotted structures will be drawn circularized by default even if this option is not specified. Default is to show a collapsed structure.
-f, -F, --flat | Specify that the structure should be drawn with its backbone stretched in a straight line. Note that pseudoknotted structures can be drawn linearized if this option is specified. Default is to show a collapsed structure.
-h, -H, --help | Display the usage details message.
-l, -L, --levorotatory | Specify that the drawn structure is rendered counterclockwise. Default is to render drawn structures clockwise.
--svg | Specify that the output file should be an SVG image file, rather than a Postscript image file. Note that only one SVG image can be written into a particular file, so the structure number flag (below) must also be specified when writing an SVG document.
-u, -U, --uncircled | Specify that no circles should surround nucleotides when drawing. Default is to surround nucleotides with circles.
### Options that require added values:
-n, -N, --number | Specify a particular structure to be output, one-indexed. Default is -1, which signifies all structures output to one file.
-p, -P, --probability | Specify the name of the file from which base pairing probability data will be read for annotation. This file must be a partition function save file generated by the partition interface. Default is no probability annotation file used.
-s, -S, --SHAPE | Specify the name of the SHAPE annotation file from which SHAPE data will be read for annotation. Default is no SHAPE annotation file used.
-t, -T, --text | Specify the name of the text file from which base pairing probability data will be read for annotation (generated, for example, by partition-cuda). This file should describe pairing data for the predicted structure, not the accepted structure. Default is no probability annotation file used.
### References: Reuter, J.S. and Mathews, D.H. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC Bioinformatics, 11:129. (2010).