Web Interface

The generated contacts_circos.html is the main analysis environment.

Layout

The page has:

  • a left control sidebar,
  • a main circos display area,
  • popups for selection editing and stored plot information.

Plot title

Editable title shown above the plot and included in SVG export.

Minimum contact visibility threshold

Controls which links are visible.

  • minimum is 1
  • links with count < threshold are hidden
  • residue interactivity follows the same threshold rule
  • autotrim uses the same threshold rule

Contact mode

  • Atom: count every atom contact row
  • Residue: count each displayed contact arc at most once per model

Minimum AF3 contact probability

This control appears only when the HTML was generated with af3FullData true and matching AlphaFold3 full-data JSON files were found.

It hides contact links whose mean AF3 contact_probs value is below the selected value. The slider range is derived from the mean contact probabilities actually mapped onto the contact dataset.

For each model, repeated atom-level contacts within the same residue pair use the maximum AF3 contact probability. Across the processed models, displayed links use the mean probability for filtering, with models lacking that displayed contact contributing zero; hover text reports both the mean and the maximum observed value.

pLDDT-colored arc saturation

This is not an interactive switch in the HTML. It appears when the plot was generated with useplddt true.

Chromosome arc colors are desaturated by residue pLDDT:

  • pLDDT near 100: normal saturated arc color
  • pLDDT near 0: gray

This affects chromosome arcs only, not contact-link colors.

Display

  • Transparency: when enabled, stronger links are more opaque; when disabled, all visible links are fully opaque
  • Default colors: when checked, use the plugin’s default plot colors; when unchecked, use captured ChimeraX ribbon colors for chromosome arcs and contact links

If no ChimeraX ribbon colors were available when the HTML was created, Default colors is disabled.

Maximum line width

Controls the upper bound of visible link thickness.

Angle offset

Rotates the plot.

If a chain is locked to the bottom, manual angle changes clear that lock.

Chain Presence/Order

This text box controls which chains are shown and in what order.

Rules:

  • chain IDs may be comma- or space-separated
  • omitted chains are hidden from the plot
  • unknown chain IDs are flagged below the field
  • remaining chains expand to fill the circle

Buttons below the field help reset the list:

  • Show contact chains: show chains with contacts in the current dataset
  • Show all chains: also include available chains that were omitted by default, such as single-atom ion chains

Per-chain rows

Each chain row includes:

  • a checkbox: show or hide links involving that chain
  • the original chain label: click once to lock that chain midpoint to the bottom
  • a direction arrow: flip arc orientation
  • a display-name text box: rename the arc label

To lock the junction between two adjacent chains to the bottom:

  1. click a chain label to lock it,
  2. click the same locked label again,
  3. click one of the temporarily cyan neighboring labels within five seconds.

Manual angle changes, hiding the locked chain, or choosing another lock clears the previous bottom lock.

Plot Interaction

Hover on an arc

Shows a tooltip for the current residue/base position.

If the hovered position has visible links at the current threshold, the tooltip background turns blue to indicate that shift-click isolation is available.

Click-and-hold on an arc

Temporarily show only links involving that chain.

Release returns to the full current view.

Shift-click-and-hold on a residue/base

Temporarily show only links involving that residue/base.

This works from either endpoint of a link.

Click a contact arc

Copies a ChimeraX select command to the clipboard.

The copied command:

  • is compact when possible,
  • uses actual contributing source residues,
  • uses the actual DNA strand/base involved in the link rather than the merged display DNA arc.

A toast appears in the plot area showing the copied command.

Region Selection

Drag along an arc to create a region selection.

Selections support overlap.

A target dot appears near the outer edge of a selection; click it to open the selection menu.

Selection Menu

The selection menu is grouped by function.

Annotations

  • Sequence callout: create a sequence callout for the region
  • Comment: create a free-text callout

Sequence callouts:

  • include the range in the title bar by default
  • append average pLDDT to the title bar when pLDDT data are available
  • show contacting residues in bold blue at the current threshold
  • stay editable after creation

ChimeraX Select

There are two region-based ChimeraX selection actions:

  • All models: copy a command selecting the whole selected region across all models
  • Contacts @ threshold: copy only residues from models/links that actually contribute visible contacts in that region at the current threshold

Range

  • Autotrim: shrink the region to the first and last residues within the region that have visible contacts at the current threshold
  • Clear: remove the selection and its metadata
  • Edit: numeric and slider controls for start/end coordinates
  • region Color: color the selected arc region overlay
  • Link color: recolor visible links touching that selection
  • Default: clear the selection-specific link color override

Callouts

Callouts are live editing objects on the plot.

Sequence callouts

  • generated from the selected sequence or DNA track
  • for merged DNA, show one strand only in the chosen display direction
  • contacting positions are highlighted in bold blue

Comment callouts

  • free-form text
  • no automatic title text
  • draggable using the top bar

Shared callout behavior

  • directly editable in place
  • draggable
  • resizable
  • connected to the selection by a leader line
  • saved in session JSON
  • exported in SVG

Export And Persistence

Download SVG

Exports the current plot state as vector graphics, including:

  • visible arcs,
  • visible links,
  • selections,
  • labels,
  • callouts,
  • styled callout text.

Save HTML

Saves a standalone interactive HTML snapshot.

This includes the current UI state and stored provenance metadata.

ChimeraX Colors

Exports a .cxc file that:

  • colors everything light gray,
  • selects residues involved in visible links at the current threshold,
  • recolors them to match the link colors.

This respects:

  • threshold,
  • count mode,
  • visible chain order,
  • per-chain link checkboxes.

Save Session / Load Session

Session JSON saves and restores:

  • thresholds,
  • count/display options,
  • chain order and flips,
  • link visibility by chain,
  • single-chain or adjacent-chain junction bottom lock,
  • selections,
  • callouts,
  • colors,
  • callout geometry.

It is intended for reapplying a view state to compatible data.

Info

The Info button opens a popup showing embedded provenance:

  • tool version,
  • timestamp,
  • invocation string,
  • model names,
  • filenames,
  • paths when available.

Copy command copies the full stored circoscontacts invocation to the clipboard.