RnamlView
RnamlView is a visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView (above). The application generates standard molecular representations (e.g. tRNA cloverleaf structures) or any structural representation desired by the user by rearranging various parts (e.g helices and single strands) of the RNAView 2D diagrams. RNA motifs are rapidly identified and classified with the base pair annotation and the 2D graphic display.
The RnamlView Project
Fabrice Jossinet, & Eric Westhof
Institut de biologie moleculaire et cellulaire du CNRS
Strasbourg, France
Introduction
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 :
- The RnaML file format
- The RnamlView tool
- The LW base pair classification
- The next orientations of this project
- Download/installation steps of our tools
- Gallery
- Some useful links
- Some references
- Contacts
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.
In order to easily view, analyze, manipulate and save rna data stored in rnaml file format, we have designed a graphical viewer implemented with the Java language. This viewer named RnamlView open a pdb or an rnaml file and construct :
- a tree representation of the RnaML file
- the rna secondary structure stored in the RnaML file
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 :
- a tree representation of the RnaML file (1A)
- the rna secondary structure stored in the RnaML file (2A)
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,...).
The RnamlView symbols display and the LW classification
The RnamlView software draws the tertiary interactions in green
In agreement with the RnaView output :
- Single dashed lines mean tertiary interactions (the pair has a single hydrogen bond or the pair has more than one hydrogen bond but with bad geometry)
- Modified nucleic acids are given as lower case letter
- The standard Waston-Crick base pairs are annotated as two closer parallel lines for GC pair and a single line for AU or AT pair
- GU wobble pairs are annotated as a circle
- All the other 12 type of non-Waston-Crick base pairs are annotated according to the table below.
- add a 3D view panel interconnected with the 2D view
- use of the different rna databases and tools with RnamlView (Zucker mfold, Blast,...)
- developement of a database dedicated to store RnamlView objets
- Prerequisites
To use RnaMLView, you need a 1.3 Java Platform installed on your system. RNAVIEW is provided as binary or source code so you can recompile it for your machine. RnaMLView and RNAVIEW have been tested and work fine under UNIX systems like Linux and MacOSX. To get the secondary structure from a pdb file, you need to be connected to Internet since the program need to parse the RnaML DTD stored at http://ndbserver.rutgers.edu/rnaml.dtd. - Download
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
Example for tcsh shell: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.
- RNAML: a standard syntax for exchanging RNA information.
- Geometric nomenclature and classification of RNA base pairs.
- The non-Watson-Crick base pairs and their associated isostericity matrices.
For any problems or questions contact f.jossinet@ibmc.u-strasbg.fr