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documented circular strands in README
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dave-doty committed Dec 15, 2020
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Expand Up @@ -26,6 +26,7 @@ If you find scadnano useful in a scientific project, please cite its associated
* [Menu](#menu)
* [Side view menu](#side-view-menu)
* [Edit modes](#edit-modes)
* [Circular strands](#circular-strands)
* [Assigning DNA](#assigning-dna)
* [cadnano file format versus scadnano](#cadnano-file-format-versus-scadnano)
* [How to design structures manually using scadnano](#how-to-design-structures-manually-using-scadnano)
Expand Down Expand Up @@ -634,6 +635,16 @@ There are different edit modes available, shown on the right side of the screen.
* **(m)ove group:**
This mode allows one to translate the currently selected helix group in the main view by clicking and dragging (i.e., to change its `position.x` and `position.y` coordinates, which can also be set manually under the menu Group → adjust current group). When in this mode, press either the Ctrl (Cmd on Mac) or Shift key and then click+drag with the cursor. (Without pressing Ctrl or Shift, the normal panning of the view will occur, without changing the position of any helix group.)

## Circular strands
It is possible to create circular strands, by ligating a strand's 5' and 3' ends, or by adding a crossover between a strand's 5' and 3' ends:

![](images/circular-strand.png)

Although this is allowed while editing strands, it is encouraged eventually to make all strands linear (non-circular) by adding appropriate nicks or deleting crossovers.
At the current time, assigning and tracking DNA sequences in circular strands is not well-supported.
In particular, there is not a straightforward way, when assigning DNA, to control where it begins on the strand.
The reason this feature is allowed is that it helps to allow circular strands as *intermediates* that will eventually be made linear.


## Assigning DNA
Right-clicking on a strand allows one to assign a DNA sequence to a strand (or remove it if assigned).
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