The S2S workflow
The S2S workflow | S2S, the RnaML file format and MFold | Home
Last update : 18th July 2005S2S can open several file formats : FASTA, PDB and RnaML. For any of these, S2S constructs an object in memory named an S2SView. This is a tree representation of all the data stored in the original file. The S2SViewer core tool provides a graphical display for the tree and allows to launch the different tools provided with S2S (Rnalign, Rna2DViewer, Rna3DViewer). Each S2S tool launched from S2SViewer uses the S2SView objet to construct its own "View" fitting its purpose. An S2S working session can be saved in an RnaML file. This saves the 2D secondary structures coordinates and the multiple alignments. If the working session started from an PDB file, S2S registers the PDB file as a comment in the RnaML file. The working session can be started again by opening the RnaML file. The PDB file indicated in the comment has to be in the same directory. Beside saving a complete working session, one can export alignments within Rnalign in FASTA or SVG files, and 2D structures within Rna2DViewer in SVG files.
S2S, the RnaML file format and MFold
S2S can open file and save data in the RnaML file format. When S2S has opened a PDB file, the tertiary coordinates are not stored in the RnaML file to avoid producing a huge-sized file. Instead, S2S saves the name of the PDB file as a comment, like :
<rnaml comment="s2s:tr0001.pdb">
The next time this RnaML file is opened, S2S will link the RnaML data with the data in the file indicated in this comment. To work, you need to have this file in the same directory as the RnaML file. S2S automatically copies the PDB file in the same location as the RnaML file.
In general, an RnaML file is associated to a document named a DTD (Document Type Definition). The location of this DTD is indicated in a DOCTYPE line. The RnaML files produced with the MFold algorithm references the DTD hosted at http://www-lbit.iro.umontreal.ca/rnaml/current/rnaml.dtd. Consequently, in order to open an RnaML file created by MFold in S2S, you need to be connected to internet. The RnaML files produced with RNAVIEW from a PDB file or produced with S2S to save your work, reference both a DTD which should be localized in the same directory as the RnaML file. I suggest you to keep your RnaML files in a directory containing a copy of the rnaml.dtd file provided with S2S. To assist you, when saving an RnaML file, S2S automaticaly copies the rnaml.dtd file from its config subdirectory to the same location as the RnaML file.