Assemble 1.0 Release Candidate 2
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Bugs fixed
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* the user was not able to browse directories when he wanted to save or export some data
* 2D edition: if an helix deleted is at the 5'-end of an RNA, the full molecule became a single-strand
* saving of an Assemble model using the textual data: it was done one directory too high
* the parser of the XPLOR format for density maps has been fixed to be able to read the files generated by the map2map tool provided by the Situs package (http://situs.biomachina.org/). For details see http://serialized-thoughts.blogspot.com/2009/06/using-saxs-data-with-assemble.html
* the refinement of the 3D model has been fixed and improved


Improvements
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* when an RNA algorithm has no solution, a dedicated message is displayed (and not an error)
* if a sequence contains an unknown modified residue, if the user doesn't know the unmodified version (A, U, G or C), he can choose "?". But to be used carefully
* a plugin system is now available (check http://www.bioinformatics.org/assemble/plugins.html for details)
* it is now possible to use the embedded paradise platform to run user-defined groovy scripts (by typing "java -jar paradise.jar" in the lib directory)
* when a selection is made from the 2D panel, the atoms are displayed automatically if they were invisible
* to load FASTA files, the suffix of the files can be ".fasta", ".fna", ".fas",".fa" or ".txt"
* an "Undo History" panel is available. When the button "Accept current 3D model" is clicked, Assemble asks for a name. This construction step will be listed in the Undo panel.
  When the user double-click on a construction step listed, the corresponding state of the 3D model is restored (for details see http://serialized-thoughts.blogspot.com/2009/05/undo-history-panel-of-assemble.html).
* the way to apply an RNA motif is more flexible. To make the link with a subsequence of an RNA motif, select a set of residues in the 3D scene, even if they're not contiguous and/or in the same molecular chain.
  One constraint: the number of residues selected has to be equal to the length of the subsequence you want to link.
* the algorithms_installation.sh script has been improved to warn the user if it is not launched from its own directory
* when Assemble starts, it checks if the user has started it from its own directory. This is necessary to manage some algoritms like the SVG export of RNAplot (at least, until we find another workaround)
* two new icons to quickly tile horizontally or vertically the two widows of Assemble
* the Map panel has been reorganized and improved
* it is now possible to modify the opacity of a density map rendered as a mesh
* the 3D model can be centered on the density map. The center of the density map is calculated according to the triangles displayed (with the mesh mode). If they change, so will the center of the map
* the 2D model can be exported in an SVG file
* Assemble can load an RNA secondary Structure stored in a FASTA file and described with the bracket notation (for details see http://serialized-thoughts.blogspot.com/2009/06/load-secondary-structure-described-with.html)