Difference and deformation density

Density loading is opt-in for the widget. Enable it when the selected CIF block contains standard FCF coefficients, observed reflections suitable for an IAM Fo−Fc calculation, or a self-described custom deformation-density loop (the concepts are explained in General → Density concepts):

<cifview-widget
    src="coordinates-and-reflections.cif"
    options='{"differenceDensity":{"autoLoad":true}}'>
</cifview-widget>

The coordinate structure appears first; reflection parsing, IAM calculation, FFT, and progressive surface generation then run in a worker by default, with a main-thread fallback where workers are not available. As soon as calculation starts, a button appears beside the ordinary display controls and shows the progressive step instead of opening a large status box. Its first row reads Δρ/eų; once complete, its second row changes to the positive/negative contour magnitude. Clicking it cycles through all loaded fields and then a hidden state without recalculating their grids. With one field this remains a hide/show toggle. It is not shown when no density is loading or available.

Live example — urea with embedded reflection data (the density button appears top right once the map is ready):

Standard difference maps use green/red wireframes by default; custom coefficient loops are treated as deformation density and use light blue/orange. See Library → Density maps for supported reflection sources and custom columns, and Options Reference → Density for contour, colour, resolution, symmetry, and worker settings.

Planar contour lines

A widget can replace the 3D isosurface with line-only contours in a molecular plane. The contour layer has no filled plane or background object, so the widget's configured page/viewer background remains visible:

<cifview-widget
    src="coordinates-and-reflections.cif"
    options='{
      "differenceDensity":{"autoLoad":true},
      "contourLines":{
        "enabled":true,
        "plane":{"atoms":["C1","C2","O1"]},
        "contourCount":20
      }
    }'>
</cifview-widget>

Use {"mode":"best-fit"} for all displayed atoms, or provide coordinateSystem, origin, and normal for an explicit Cartesian or fractional plane. During progressive loading, field sampling and Marching Squares run in the scalar-field worker; the UI thread only installs the packed line segments. The same density button continues to hide/show or cycle loaded fields.

A live contour example is in the Gallery → Contour section.