Usage

Menu | Input format  | Editor  | Web application for any systems
New: create a new file of structure data.
Open File:
: open an existing file of brakect format.
: open an existing file of paired positions.
: open an existing file of PairAnalyzer result.
Open Example Data: open an example of structure data.
Open Selection: open the selected part in a new window.
Close: close the current file of structure data.
Save Structure Data:
: save the structure data in the current file.
: save the structure data in a new file.
Save Structure Drawing:
: save the entire structure image.
: save only the structure image shown   in the window.
Structure data: Structure data window On/Off.
Thumbnail: Thumbnail window On/Off.
RNAs: list of RNAs visualized.
Topological relation: Topological relation window On/Off.
Fit on window: Resize the image to fit in a window.


Default size: show bases by their default size.


To center: move the structure image to center.
Edit images
This menu is also available as a popup menu when you click the mouse right button in the structure image window. The undo and redo functions are new in PseudoViewer3 for cancelling and redoing the last operation on the structure.

To edit a stem-loop, first select the stem-loop as follows.
Pseudoknot: Click the stem of the pseudoknot. (enclosed in squares below).
Loop: Click the corresponding loop.

Rotate All:
íŠ

Rotate a loop:
To rotate a pseudoknot, first select a pseudoknot and drag it.
íŠ

To rotate a loop, first select a loop and drag it.
íŠ

Scale All: Resize the entire structure image.

Scale a loop:
Example 1
íŠ
 
Example 2
íŠ

Move All:
íŠ

Move Numbering:
íŠ

Loop type

A loop can be drawn either as an arc or straight line. Click the loop and choose the line type. Default is an arc line.
Select a loop
Loop as straight line
Loop as arc line

The loop as straight line can be moved and rotated.
Move a straight loop

Rotate a straight loop
The loop as straight line can be rotated by moving opposite ends of the loop. In this case, the corresponding menu is 'Rotate a loop'.


Flip horizontal:
íŠ

Flip vertical:
íŠ
Display options allow you to change drawing options.

reDraw: Refresh the current structure image.
default:

 
off Standard View:

 
off base pair:

no base numbering:


PK Highlight
On:
Off:

Outline:
On:
Off:

Additional line:
structure data (((((:::[[[[::{{{{)))))::]]]]::}}}}
On:
Off: