RNAView

RNAView generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions. RNAView automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures, fully implementing Leontis and Westhof's ( RNA (2001) 7, 499-512), convention for edge-to-edge hydrogen bonding interactions.

This program's output can be used by nuccyl to generate PyMOL figures.

To use RNAView for Linux, SGI, or Mac OS X:

• Type:

  setup rnaview

• To generate fully annotated base pair lists:

  rnaview [your_pdbfile]

• To generate a fully annotated 2D structure in Postscript format, with accompanying detailed information in XML format:

  rnaview -p [your_pdbfile]

• To generate a 3D structure in VRML format, viewable with a VRML web browser plugin:

  rnaview -v [your_pdbfile]

• To select only particular chains for calculation (e.g., to produce only a single chain output from a dimeric structure), add the -c flag. For instance:

  rnaview -pc [chain IDs] [your_pdbfile]

• To process many PDB files, place the filenames into another file, e.g., file.list, with the names separated by a space. Then process this file with the -a flag. You may optionally give a minimum resolution to accept. For instance:

  rnaview -a file.list 3.0

  will only process PDB files in filelist with better than 3.0 Angstrom resolution.
• If you already have an XML file from some other nucleic acid tool, use the -x flag to input it into rnaview:

  rnaview -px [your_xmlfile]

The above documentation is also available by typing:

rnaview -h

Example PDB files may be found in $RNAVIEW/test. Copy these to another directory if you wish to experiment.

If you use this program in a published report please cite the following:

Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H.M., Westhof, E. (2003). Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Research 31 (13): 3450-3460.