Usage:
sop operation arguments

The sop command performs operations on one or more surface models. The operation can be:

• cap - adjust capping of clipped surfaces
• clip - spherically clip volume isosurfaces, with curved caps
• finerMesh - subdivide surface mesh
• hideDust - hide small blobs (disconnected parts)
• hidePieces and showPieces - hide/show specified pieces (independently selectable parts)
• transform - scale, rotate, and shift surfaces
• zone - show only surface parts within a cutoff distance of specified atoms

Operation keywords and their sub-keywords described below can be truncated to unique strings, and their case does not matter. Surface models can be specified by a model number or range of model numbers preceded by #, or simply # to indicate all applicable surfaces. Synonyms for true: True, 1. Synonyms for false: False, 0. A vertical bar "|" designates mutually exclusive options, and default settings are indicated with bold.

See also: surface, scolor, setattr, volume (surface and mesh options), surface attributes

Adjust capping, in which planar caps are drawn to hide the interior of a surface model sliced by a clipping plane. Capping can be toggled on or off, and caps can be shown as a solid surface or as mesh. The offset distance d is how far to displace caps from the clipping plane (default 0.01 Å). Some displacement is needed, or 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. The subdivision factor f indicates how finely to subdivide cap surfaces (default 1.0, triangles approximately the same size as in the surface being capped); larger values yield smaller triangles and finer color gradations (when the cap is multicolored, for example with Surface Color), but increase computational demands. There is no reason to increase the subdivision factor when caps are a single solid color. The cap color can be the same as that of the clipped surface model (details) or indicated with any color name that specifies a single color. See also: Surface Capping

Spherically clip volume isosurfaces, with curved caps covering holes. The clipping sphere center and radius can be specified; defaults are the geometric center of the isosurface and 40% of the largest dimension of its bounding box, respectively. The coordinate system for interpreting center x,y,z specifications is indicated by reference model ID number preceded by #. Caps can be shown as a solid surface or as mesh. Cap color defaults to the same as the isosurface, but can be indicated with any color name that specifies a single color, except with spaces collapsed (e.g., hotpink instead of hot pink). The replace option indicates whether to remove any pre-existing spherical clipping caps.

Subdivide the surface mesh to achieve the specified vertex spacing d. If the input surface already has a finer mesh than what is specified, it will simply be duplicated.

Hide smaller blobs (disconnected parts) of a surface. One use is to simplify the display of noisy volume data. The cutoff size for hiding must be specified; blobs smaller than s will be hidden, where the units depend on the metric:

• size (default) - bounding box dimension (largest of X, Y, Z)
• area - surface area
• volume - enclosed volume
• sizeRank - rank by largest size (a value of N indicates showing the N largest blobs by the size criterion)
• areaRank - rank by largest area
• volumeRank - rank by largest volume

Size measurements will include any blob parts that have been undisplayed or hidden by zoning or clipping, and blobs at or above the cutoff size will be displayed completely (although possibly still clipped) even if they had been hidden beforehand. The update option indicates whether to update hiding automatically if the surface is changed (default true). The command ~sop hideDust stops hiding blobs of the specified surfaces. See also: Hide Dust

Hide and show pieces (independently selectable parts) of a surface. Surface pieces can be specified by model number or as a selection (details...).

Scale, rotate, and shift surface models and/or pieces. Surface pieces can be specified by model number or as a selection (details...). Scaling about the center is applied first, then rotation about the center and axis, and then translation (shifting). Scaling can be done with a multiplicative scale factor s, or such that the largest distance from a surface vertex to the center is radius r (see the video mini-example). The rotate option indicates a rotation of angle degrees about the center and axis, and move indicates a shift of x, y, and z distance units along the X, Y, and Z axes, respectively. The center for scaling and rotation defaults to the area-weighted center of the surface, but can be given as x,y,z coordinates or an atom-spec. The rotation axis can be given as:

• x - X-axis
• y - Y-axis
• z (default) - Z-axis
• x,y,z (three values separated by commas only) - an arbitrary vector
• an atom-spec of exactly two atoms (not necessarily bonded or in the same model) or one bond. A bond can only be specified by selecting it and using the word selected, sel, or picked; any atoms also selected at the time will be ignored.

The coordinate system for interpreting center, axis, and shift x,y,z specifications is indicated by reference model ID number preceded by #. By default, the coordinate system of the first specified surface is used.

Show only parts of the surface within radius Å of any atom in atom-spec. If bondPointSpacing s is specified, use points along bonds in addition to the atoms to define the zone. The points along the bonds will be placed s × (bond radius) apart. Link radii in Volume Tracer are equivalent to bond radii, except when a link radius is 0.0, the corresponding bond radius is 1.0. The maxComponents option indicates hiding all but the N largest connected surface patches in the zone; by removing the visual clutter of small patches, this can significantly enhance viewing of pocket surfaces. Ranking to determine the largest is based on maximum dimension (along X, Y, or Z for a given patch), including any portions within the zone that are hidden by clipping. If maxComponents is not supplied, all patches within the zone will be shown. The update setting indicates whether to update the zone automatically if the surface changes shape. The command ~sop zone stops hiding the surface parts outside the zone. See also: Surface Zone

The following options apply to operations that create a new surface model.

modelId N
Open the new surface as model number N (an integer, optionally preceded by #). The default is the lowest unused number.

inPlace true|false
Whether to overwrite the existing surface in Chimera instead of creating a new one.