Surface Capping

Surface Capping draws planar caps that hide the interior of a surface model sliced by a clipping plane. Surface Capping information is included in saved sessions. See also: Surface Color, Color Zone, clip, mclip

There are several ways to start Surface Capping, a tool in the Depiction and Surface/Binding Analysis categories. It can also be called from the Side View and Per-Model Clipping dialogs, and is implemented as the command sop cap.

• Cap surfaces at clip planes - whether to show caps
• Use cap color [color well] - whether to use the color well color for caps. Otherwise, cap color will be:
  • for molecular surfaces, the model-level color of the corresponding molecule model (see coloring hierarchy)
  • for other surface models, the surface color in single-color mode
  This option is ignored when caps are colored with Surface Color.
• Cap style
  • solid (default)
  • mesh
• Mesh subdivision factor [f] - how finely to subdivide cap surfaces. By default, f=1.0, which makes cap triangles approximately the same size as triangles in the surface being capped. Larger values of f yield smaller triangles and finer color gradations (when the cap is multicolored with Surface Color), but increase computational demands. There is no reason to increase the subdivision factor when caps are a single solid color. The number of cap triangles scales as f ²; a very high subdivision factor (f>10) can make cap calculation extremely slow and cause Chimera to run out of memory and crash.
• Cap to clip plane distance [d] - the cap must be offset at least slightly from the clipping plane (d=0.01 by default). Without an offset, the cap itself can be clipped (invisible) depending on floating-point rounding errors and the specific graphics hardware being used. If d is large, however, the mismatch between the cap and the cut edge of the surface will be evident.

Lack of per-model settings. The settings apply to all surfaces. It is not possible to cap one surface but not another, or to use different colors, styles, or other capping parameters for different surfaces. This is a limitation of the user interface, not the underlying implementation.

Slow interactive rotation. Rotating the model causes the cap calculation to check if the near clipping plane intersects the surface at each frame of the rotation. This can slow down interactive rotation.

Artifacts in cap. Artifacts such as streaks and dots in a cap can occur when points in the border are very close together. Slight changes in the surface shape or the position of clipping plane relative to the surface will generally solve the problem.

Surfaces with a boundary. The cap calculation assumes that the intersection of the clipping plane and the surface forms closed loops. If the surface has a boundary (for example, a isosurface might end abruptly at the edge of the corresponding volume data), then its intersection with the clipping plane may form a non-closed curve, which will not be capped. The basic difficulty in this case is that the surface does not separate its interior from its exterior.