How to rearrange a drawing

A drawing produced using a skeleton is not always entirely publication quality and will probably need some minor editing. If you have made a larger structure drawing without using a skeleton, it will almost certainly need a lot of editing (rearrange overlapping areas, etc.)

Minor rearrangements

Selection
Minor rearrangements are best done in the "element selection mode". In this mode, clicking on a base will select the structural element (helix or single strand) the base is a part of. The selection will be indicated in red and with a red bounding rectangle.

Elements can be added or removed from the selection by clicking on one of their bases while the "Control" key is pressed. The "select tree" option in the "Edit" menu expands the selection to include all bases enclosed by the selected helices. You can also select the entire drawing (Select drawing) to reposition it on the page.

Moving
Dragging a single strand base in the will rearrange the single strand so that it runs throught the new position of the dragged base. The entire selection can be moved by simply dragging a helix base with the mouse. The single stranded areas connecting the selection to non-selected parts will be automatically redrawn. Although the result is usually quite reasonable, large rearrangements can lead to less pleasing connections. These can be rearranged easily by dragging one of their bases to a better position.

The "single selection mode" is different here as it treats all object equally. There is no automatic selection of other objects then the one clicked on, and no automatic rearrangements: Using this mode, each object can be positioned individually if necessary.

Rotating
You can set RnaViz to rotation mode using the "Rotate" entry in the "Mode" menu, using its key shortcut (usually r) or by clicking on the rotate button. Repeating this action will turn off rotation mode. In rotation mode, dragging any base of the selection will rotate the selection in stead of moving it. The center of rotation is indicated by a target, which can be repositioned by dragging it with the mouse.

You can also orient the current helix (the one which has the current item) in a given direction using the "Geometry toolbar" or "Orient" options in the "Geometry" menu. The selection will be rotated together with the current helix.

Geometry
The "Geometry" menu has several options which can be very useful when arranging a structure. The "Orient Helix" was already described in the previous paragraph. Some of these options are:

In the "Options" menu, you can find alternate ways to display structural elements:

Hints

Larger rearrangements

For large rearrangements the "tree selection mode is often more appropriate. Clicking on a base of a helix will select the entire domain enclosed by this helix.

The easiest way to unentangle an overlapping structure is usually to first select some of the largest domains (by selecting the base helix), move these appart and orient their base helices using Geometry toolbar or the key shortcuts for the most common directions given in the "Geometry.Orient" menu. Continue by working gradually to the smaller domains. You can use the "Escape key" to deselect everything.