Troubleshooting¶

The browser opens but the plot seems empty¶

Check the most common causes first:

• threshold is too high
• the relevant chains were removed from Chain Presence/Order
• the per-chain link checkbox is off for one or both participating chains
• Residue mode is selected when you expected dense Atom-mode links

The HTML says Render status: pending¶

Use a current build.

Older intermediate builds had a generated-JavaScript error that could prevent the page from initializing.

The DNA arc does not look right¶

Possible causes:

• DNA merge detection did not match the input layout
• a split/nicked duplex needs dnaMismatches adjusted
• you may want dnaMode split for diagnosis

Try rerunning with:

circoscontacts dnaMode split

If that looks correct, the issue is in merge interpretation rather than missing chains.

Clicking a contact arc does not select what I expected¶

Remember:

• the copied ChimeraX command is based on the real contributing source residues,
• merged DNA display arcs do not copy as a pseudo-chain,
• the actual strand/base residues are used when available.

Default colors is disabled¶

This means the HTML was created without usable ChimeraX ribbon colors.

Current plugin behavior reads ribbon/cartoon colors, not arbitrary other coloring sources.

If you want arc colors to follow the structure view:

1. apply ribbon colors in ChimeraX first
2. then run circoscontacts

My Coulombic or hydrophobic coloring did not appear on the arcs¶

Those schemes are only captured if they end up as ribbon/cartoon colors on residues.

They are not currently read from:

• surface-only colors
• atom-only colors
• map data by itself

Session JSON will not load¶

Use a session file produced by the current tool.

Current accepted schemas:

• contacts-circos-session-v1
• contacts-circos-session-v2

Invalid or unrelated JSON files will be rejected.

Saved HTML opens, but I want to know exactly how it was created¶

Use the Info button in the HTML.

It shows:

• tool version
• timestamp
• invocation string
• source model metadata

ChimeraX Colors does not recolor the residues I expected¶

Check:

• threshold at export time
• chain order / chain inclusion
• per-chain link checkbox state
• count mode
• whether the structure currently loaded in ChimeraX matches the original chain IDs and residue numbering