oxDNA export issue

[ben-s-e]

When I load this cadnano JSON design into scadnano, there seems to be 3 problems.

1. The main grid view has irregularly spaced rows
2. The design will not allow assignment of a scaffold sequence. When I try to assign predefined M13 p7429 scaffold, it says: "s1=CTGGAAG and s2=???????? are not the same length."
3. When exporting the design to oxDNA format, the .top file produced seems to have 6 staple strands which are 1 base too long. Below is a list of ascending strand lengths in the .top file produced:

[3, 20, 20, 20, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 35, 35, 35, 35, 35, 35, 38, 38, 38, 38, 38, 38, 40, 40, 40, 42, 42, 42, 43, 43, 43, 43, 43, 43, 44, 44, 44, 2410]

Conversely, when a .top file is produced by converting the original cadnano JSON file to oxDNA, via the tacoxDNA tools, this is the list of ascending strand lengths in the .top file produced:

[3, 20, 20, 20, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 35, 35, 35, 35, 35, 35, 37, 37, 37, 38, 38, 38, 40, 40, 40, 42, 42, 42, 42, 42, 42, 43, 43, 43, 44, 44, 44, 2410]

Note that strand lengths in the scadnano .sc file DO agree with those in the .top file produced via cadnano -> oxDNA via the tacoxDNA tools. It seems to be an issue in the scadnano oxDNA export for this design.

[dave-doty]

Sounds like this is a few different issues.

The Python library has import/export code for cadnano and oxDNA, so I'll open issues there and point to this one.

1. The main grid view has irregularly spaced rows: see cadnano import should use helices_view_order to preserve the main view ordering of helices as they appear in cadnano scadnano-python-package#202
2. The design will not allow assignment of a scaffold sequence. When I try to assign predefined M13 p7429 scaffold, it says: "s1=CTGGAAG and s2=???????? are not the same length.": fix crash error in assignment of DNA to design with deletion on one domain but not other scadnano-python-package#203
3. When exporting the design to oxDNA format, the .top file produced seems to have 6 staple strands which are 1 base too long. Below is a list of ascending strand lengths in the .top file produced: Update: Seems to have been a bug dependent on the previous one; fixing the deletions so they come in pairs fixed this also.

[ben-s-e]

Here is the original design in cadnano v2, from paper "An easy-to-prepare mini-scaffold for DNA origami", Brown et al. 2015: https://pubs.rsc.org/en/content/articlelanding/2015/NR/C5NR04921K

And a close-up of the deletions in one portion of the design. Exactly 6 deletions in the design (2 in each of the triangle sections) fall on the 3' end of staple strands.

[dave-doty]

@ben-s-e I want to point out that this design is ideal for using helix groups to help display in 2D more like how the structure actually appears. I'd put helices 0,1,2,3,4,5 in one group, helices 12,13,14,15,16,17 in another, and helices 22,24,25,26,27,28,29,31,33 in another. Then rotate two of the helix groups by setting their pitch fields (in units of degrees that rotate clockwise). Finally, use the "move helix groups" edit mode (bottom button under edit modes) to Ctrl+click+drag to translate the helix groups to where you want them.

This will get a bit easier after I implement this feature, which I realized is lacking and would make this process faster: #679 Currently, you would have to add new helices to the new groups, then select the domains on helices in one group and drag them to move them to the new group.

Here's a quick mock-up (zipped scadnano file here):