# The Program `RNAplot`

## Introduction

You can manually add additional annotation to structure drawings using the `RNAplot` program (for information see its `man` page). Here’s a somewhat complicated example:

    $ RNAfold 5S.seq > 5S.fold
    $ RNAplot --pre "76 107 82 102 GREEN BFmark 44 49 0.8 0.8 0.8 Fomark \
      1 15 8 RED omark 80 cmark 80 -0.23 -1.2 (pos80) Label 90 95 BLUE Fomark" < 5S.fold
    $ gv 5S_ss.ps

## PostScript macros

`RNAplot` is a very useful tool to color structure layout plots. The `--pre` tag adds PostScript code required to color distinct regions of your molecule. There are some predefined statements with different options for annotations listed below:

Command | Description
--- | ---
`i cmark` | draws circle around base i
`i j c gmark` | draw basepair i,j with c counter examples in grey
`i j lw rgb omark` | stroke segment i…j with linewidth lw and color (rgb)
`i j rgb Fomark` | fill segment i…j with color (rgb)
`i j k l rgb BFmark` | fill block between pairs i,j and k,l with color (rgb)
`i dx dy (text) Label` | adds a textlabel with an offset dx and dy relative to base i

Predefined color options are `BLACK, RED, GREEN, BLUE, WHITE` but you can also replace the value to some standard RGB code (e.g. 0 5 8 for lightblue).

To simply add the annotation macros to the `PostScript` file without any actual annotation you can use the following program call

    $ RNAplot --pre "" < 5S.fold

If you now open the structure layout file `5S_ss.ps` with a text editor you’ll see the additional macros for `cmark`, `omark`, etc. along with some show synopsis on how to use them. Actual annotations can then be added between the lines:

    % Start Annotations

and:

    % End Annotations

Here, you simply need to add the same string of commands you would provide through the `--pre` option of `RNAplot`.