- 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:
- Flip:
mirror a helix; this can be very useful for drawing pseudo-knots
- Redraw helices:
redraw the selected helices (e.g. if you have messed them up badly)
- Straighten base (or top):
arrange the bases of the current single stranded area in a straight line. I the
current object is part of a helix a helix, the 2 single strands at the base (or
top) of this helix are arranged in a line.
In the "Options" menu, you can find alternate ways to display
structural elements:
- Show double strand by connection: The current helix segment
will be displayed by drawing a box around the bases, and connecting them with a line. The
default display of a helix can be restored using the "Redraw helices" option in the "Geometry" menu.
- Unformatted Single: An area of unknown structure is by
default displayed as a single stranded area. The unformatted option will display the sequence
in this area as a text, with connections to the rest of the structure. The option "Reformat
single" restores the default display.
- Hints
-
- The undo function called from the "Edit" menu can be very useful if you
did something wrong.
- Sometimes you will have to zoom in to be able to see what you are doing.
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.