Command-Line Specification: Points, Vectors

Many commands require or optionally use specifications of points or vectors in 3D coordinate space.

In general, a point-spec can be:

x,y,z (three values separated by commas only) – an arbitrary point
a specification of atoms, residues, and/or models open in ChimeraX – the center of the bounding box of the specified items. A map's bounding box encloses its contour surface (if the map is in the surface or mesh display style) or its entire grid (when the image or “volume” display style is used).
cofr – the current center of rotation
camera – the viewer position

The default coordinateSystem for interpreting point specifications varies by command, and could be that of a specific data model or the scene coordinates.

In general, a vector-spec can be:

x – unit vector along the X-axis (1,0,0)
y – unit vector along the Y-axis (0,1,0)
z – unit vector along the Z-axis (0,0,1)
x,y,z (three values separated by commas only) – an arbitrary vector
the specifier (e.g., model number) of a previously defined axis model
an atom-spec of exactly two atoms, not necessarily bonded or in the same model
For rotations, the order of the two atoms defines a handedness, and right-handed rotations are positive. If a center point is not specified separately, it will lie on the atom-atom axis. If a center is specified, only the direction of the axis will be used. The first model in the axis atom-spec will be used for reference frame pinning unless a center point atom-spec or a coordinateSystem is also given.

The default coordinateSystem for interpreting vector specifications varies by command, and could be that of a specific data model or just screen coordinates (X horizontal, Y vertical, Z in/out of screen).