Design Checks Reference

Foldnano checks designs at a few points: when it opens a file, while you edit (the Design checks button in the strand view, see Creating A Design), and before a simulation or cadnano export. This page lists every check in one place.

Each problem has a level:

Level	Meaning
Error (red)	That export or that plugin can't work with the design until you fix it. When you open a design, errors are only reported; the design still opens.
Warning (amber)	Something will be lost or changed. You can go ahead anyway.
Info	Data the target format doesn't store. Listed, never blocking.

Opening A File

cadnano files

What Foldnano finds	What happens
A base claims a connection from a base that is empty	Repaired: the claim is removed and the base becomes a free end, as cadnano draws it. A warning names the helix and base.
A crossover end that points at its own base (some older files)	Repaired silently: rewritten to the neighbouring base, the form Foldnano writes. Nothing changes in the design.
A deletion (skip) on a crossover base	Moved to a neighbouring base. A warning names both positions. If no neighbour is free, it stays and simulation export may refuse it.
An insert on a crossover base	Kept, and reported by the Editor rules check below.
A helix length that fits both honeycomb (21) and square (32), such as 672	Foldnano picks the lattice whose crossover positions match. If the file has no crossovers to go by, you choose. A link can answer in advance with `&lattice=honeycomb` or `&lattice=square`.
Two bases that disagree about how they connect	Not opened.
Two helices on one lattice position, a negative helix number or lattice position, helices of different lengths	Not opened.
Malformed data: missing arrays, connections to helices or bases that don't exist, a base marked as both skip and insert, invalid colors	Not opened.
A strand only one base long	Not opened. Extend or remove it in cadnano first.
A helix length that fits neither lattice	Not opened.

Foldnano files

What Foldnano finds	What happens
Helices at negative lattice positions	Repaired: the region is moved onto the grid without changing where it sits in 3D. For a design saved in this browser, the unrepaired copy is kept in Backups.
A mirrored plane, from regions created on the Side (YZ) base plane before this was fixed (and never rotated since)	Repaired: the plane's V axis is flipped. The 2D view is unchanged; in 3D the regions on it flip along V, and their helices now twist the right way, so crossovers line up in the 3D view and in oxDNA/mrDNA export. For a design saved in this browser, the unrepaired copy is kept in Backups.
Inconsistencies from an earlier bug (strands listed on the wrong helix, one-way connections)	Repaired, with a message listing what was fixed (and a Backups copy for a design saved in this browser).
Anything in the Editor rules check	Reported, not changed.

Editor Rules

States the editor doesn't create itself. They come from imported files or plugin results. When you open a design, they are listed in one message. A plugin whose result has an error is refused before you can apply it.

Check	Level	What to do
A skip on one strand and an insert on the other (or different inserts) at the same base	Error	Make both strands match: remove the skip or insert and add it again with the skip or insert tool.
A skip or insert on a constrained crossover site	Error	Move the skip or insert to a neighbouring base.
Two helices on the same lattice position	Error	Move one of them.
A helix at a negative lattice position	Error	Foldnano moves a saved design onto the grid when it opens it, so this mostly shows up as a refused plugin result: fix the plugin.
A helix whose number is even on an odd lattice position (or the reverse)	Warning	cadnano export and crossover positions assume they match. Recreate the helix in place if you need either.
A freeform helix whose saved direction or roll is not a proper frame (not unit length, or roll not at a right angle to the helix)	Warning	The 3D view and exports would distort the helix. Select it and set its Roll in the Select panel, which rebuilds the frame.

Simulation Export

What oxDNA and mrDNA export (and the 3D view's NT mode) refuse. Turn on Simulation export in the Design checks button to see them while you edit. See Simulation And Export.

Check	Level	What to do
Any Editor rules error about skips or inserts	Error	As above.
A skip or insert on a base where only one strand exists	Error	Single-stranded DNA simulates fine, but not as a one-sided skip or insert. Draw the bases as ordinary strand bases (or shorten the strand instead of skipping), or remove the skip or insert.

Cadnano Export

What cadnano JSON can't hold, for the active region. Shown before Export as cadnano JSON and before a plugin that works on cadnano JSON runs. Turn on Cadnano export in the Design checks button to see them while you edit. See Exporting cadnano JSON.

Check	Level	What to do
A freeform region	Error	cadnano only has honeycomb and square lattices. Use Foldnano JSON instead.
A connection from a cadnano scaffold path to a staple path	Error	cadnano keeps those in separate arrays, decided by helix number and strand. Reroute the connection so it stays on one kind of path.
A helix length that isn't a multiple of 21 (honeycomb) or 32 (square)	Error	Change the region length.
A Editor rules issue about lattice positions or per-strand skips and inserts	Error or warning	As in Editor Rules.
A helix length that fits both lattices, such as 672	Warning	cadnano asks whether the design is square when it opens the file; the message says what to answer.
Connections to other regions	Warning	They are cut in the exported file.
Repeat-group copies	Warning	Only the originals are exported.
Sequences, modifications, oligo names, the scaffold label	Info	Not stored in cadnano JSON.

A plugin that only reads the design (no result to apply) is only stopped by errors. A plugin that replaces the region also shows the warnings, because applying its result makes those losses permanent.