RnaViz  Guided Tour

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Drawing and arranging a structure

When given a DCSE alignment file or ct file, RnaViz will ask for a skeleton file. It will then draw the structure contained in the file using the given skeleton. (RnaViz can also draw structures without a skeleton, but for larger sequences this produces drawings with many overlaps, that can require quite some work to be arranged pleasingly.) As shown in the figures of rRNA, large and complex structures can be drawn. The drawing can be rearranged interactively by selecting and dragging one or more helices. The connecting single strands will be rearranged automatically. Single strands can also be rearranged by dragging one of their bases. A helix can be oriented in a specific direction from the menus. The selected objects can also be rotated by setting the program to rotation mode and dragging any part of the selection. Different selection modes allow easy selection of either entire domains, helices, helix segments or single bases.

Clicking on a base will select the entire helix.

Select the geometry toolbar

Select orientation right: the helix is oriented, and the connecting single stranded areas are adapted You could also select the rotation tool to turn the helix manually

Select the helix by clicking on a base

And drag to another position to move the helix; the single strands are automatically adjusted

The single strands are not quite right yet: select a base of the single strand

and drag to the correct location

Peter De Rijk