Our goal is to improve the diffusion, manipulation, storage and visualisation of the RNA data. To do that, we develop informatic tools supporting the RnaML file format.
You can find on this page informations about :

In order to improve information exchange in biology, the XML format is now largely used in this field of research.

The RnaML syntax was designed to easily express data on RNA sequence and structure, and to allow the transmission of information among the RNA community. The syntax is the result of a collaborative effort between researchers active in the field of RNA structure and computer science.

RnamlView is not able to calculate a secondary structure. It generates a dynamic representation of a secondary structure already stored in an RnaML file.

RnaView is a tool developed at the NDB laboratory (Rutgers University, NJ, USA). It generates a secondary structure from an Rna tertiary structure stored in a PDB file and identifies all the base pairs present in this structure. Therefore, the couple RnamlView-Rnaview allows to easily view and manipulate a Rna tertiary structure. All the base pairs found by RnaView are graphically represented with symbols in agreement with the LW classification.

You can find below a screenshot of RnamlView with :

The 1B and 2B panels will be used to give more informations on elements selected on panels 1A and 2A respectively and to set properties for these elements (color, value,...). These graphical widgets are functional but are still under development.

The secondary structure generated by RnamlView is dynamic. The toolbar below the drawing panel allows a user to manipulate it.

	1	to select an helix and to drag the helices selected. You can select several helices if you use the shift key. You can unselect some helices with the ctrl key.
	2	to rotate the helices selected. With the shift key the rotation angle will be of 5 degrees
	3	to center the molecule on the drawing surface
	4	to flip the helices selected
	5	to zoom +
	6	to zoom -
	7	to show the LW classification symbols
	8	to hide the LW classification symbols
	9	to show the tertiary interactions
	10	to hide the tertiary interactions
	11	to save the picture as SVG or PS file

With the File -> Open menu, you can open a PDB or an RnaML file. By opening a PDB file, RnamlView will call RnaView to generate the corresponding RnaML file which will be parsed by RnamlView.

You can save your work either as a complete RnaML file (File->save menu) or only the drawing as a PS or SVG file. The PS export is done by RnaView and the SVG export is done by RnamlView. SVG files can be opened with Adobe Illustrator 10 for example or inside a browser with the good plug-in. With SVG files inside Adobe Illustrator you can modify your drawing with special tools not provided by RnamlView.

To save, it's necessary to give the suffix of the type you want (.ps, .rnaml, .svg,...).

In agreement with the RnaView output :

Download RnamlView, click the link : RnamlView_1.0-RnaView.tar.gz

Installation

Unpack the program package in your home directory (for example /home/skynet/share/) by typing :

tar -xzvf RnamlView_X.X-RnaView.tar.gz

That will create an RnaMLView directory on your system. It's important to put this directory where you have rights to write files. The RNAVIEW program uses temporary files to work.

The JAVA_HOME variable needs to be defined. This variable defines the directory where you have installed your Java platform.

Define the RNAMLVIEW environment variable corresponding to the directory you have just created.

Example for bash shell:

export RNAMLVIEW=/home/skynet/share/RnamlView_X.X-RnaView

setenv RNAMLVIEW /home/skynet/share/RnamlView_X.X-RnaView

Start the program

Run the rnamlview.sh script from the RnaMLView directory by typing: rnamlview.sh start (you can put the rnamlview.sh file in your PATH)

To open a file, it's necessary to have the "rnaml.dtd" in the same location (RnaMLView is compatible with the 1.0 RnaML DTD). I suggest you to keep your RnaML files in a directory containing a copy of the rnaml.dtd file provided with RnaMLView. Open a PDB file where you have rights to write since RNAVIEW generates a "base_pair_statistics.out" file in parallel to the RnaML file.

If you have any problems, you can generate a report of your configuration by typing : rnamlview.sh report. That will generate a report.out file in you home directory. Send me this file by email with your problem description attached.