If this file is an RnaViz structure file, the structures in that file will be loaded on the page. Structures already on the page will remain fully editable. They can be deleted by selecting them (click on one of their bases) and use the 'Delete object' option of the Edit menu (or just press delete). To remove all structures from the page the 'Clear Page' option in the File menu can be used.
RnaViz will also recognise files in the ct or DCSE
alignment format. A DCSE alignment should at least contain one sequence
line (with structure symbols) and a "Helix numbering" line. Optionally a
"mask" line can be present; the letters in the mask line will be associated
as tags to the base on the same position.
WARNING: the secondary structure parser in RnaViz is somewhat pickier
about the location of helix numbers in the DCSE alignment format than
versions of DCSE <4, eg. the helix number must always come on a position after
the helix opening symbol ([) in a sequence.
If the file is in the ct or DCSE alignment format, the user is prompted for a skeleton file. This is a file containing the layout of the structural elements in a previously made, structuraly similar drawing. The use of skeleton files makes it very easy to create a lot of drawings using the same layout. If this dialog is closed without choosing a skeleton file, no skeleton is used. Since RnaViz does not try to produce non overlapping drawings, a structure drawing produced without a matching skeleton file will usually take more manual laying out afterwards. Once a structure of a certain molecule has been layed out, it's skeleton can be saved and used for similar molecules.
All structures in the file can be loaded straight into the same page, or as a batch job saving each structure to a different file.
Depending on the selection mode, selecting a base can cause the helix segment or the entire helix the base is part of to be selected as well. Event the entire tree starting from this helix can be selected this way.
The selected part of a structure can be rotated, flipped or redrawn. Single stranded areas can be straighthened or arched or drawn unformatted.
Peter De Rijk
tel.: 32-03-820.23.16
fax: 32-03-820.22.48
E-mail: derijkp@uia.ua.ac.be
web: http://rrna.uia.ac.be/~peter/personal/peter.html
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