RNA Movies - Manual

The original RNA Movies, which is available for download, is available for Unix-like systems only. The new Java version is available for the Microsoft Windows platform as well.
The online version of RNA Movies is available as applet (embedded into a website that features a submission form) and WebStart application.

Menu and Toolbar

Most functions are self explainatory. The tool bar at the bottom of the applet provides the following functionality (from left to right):

• Open movie
• Play movie
• Stop movie
• Skip one frame back
• Skip one frame

File:

Open ...

Open a movie in DSCE/RNM format

Import ...

Import a movie in RNAStructML format

Export ...

Export current movie as PNG/JPEG/SVG/(animated)GIF

Configure...

Show the configuration panel

Movie:

Play

Start the animation

Stop

Stop/Pause the animation

Previous

Step one frame back

Next

Skip one frame

Goto Frame...

Goto a specific frame

View:

Zoom In

Zoom in by 25%

Zoom Out

Zoom out by 25%

Reset view

Reset zoom, rotation and moving

Help:

About...

Show references/credits

Mouse actions:

Left button

Move

Right button

Rotate

Mouse wheel

Zoom

Security

As mentioned before the 'online' RNA Movies client is written in Java language and runs as an applet in your browser's restricted enviroment called sandbox. The access control policies of such an enviroment are typically restricted in many ways. In general applets cannot write files. Therefore we have digitally signed the applet to enable users to use its import and export functionality. This means that a warning dialog asks the user to accept the applet's signature. For now we use a selfmade security certificate which is not trusted.

Input data format

Since release 1.2 RNA Movies supports two input formats. The RNAfold / Vienna format and DCSE format. Both formats have been extended to include pseudoknots, entangled helices, and structure description. The RNM format is simpler and more intuitive while the DCSE format has more possibilities. The current version (2.x) supports additionally to its own format the DCSE format and RNAStructML as input format.

• RNM (RNAFold/Vienna) Format:
  The first two lines are similar to the FASTA format:
  First line: > description (ignored, the leading '>' is needed to determin the input format)
  Second line: RNA sequence (needed for labeling)
  Following lines: structures (pairing bases represented as pairs of parantheses - () for normal and [] {} <> for pseudoknot bonds, unpaired regions are denoted as dots)

Some Examples