### 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,
interpreted in scene coordinates
unless a different **coordinateSystem** is given
- an
*atom-spec*
– the center of the bounding box of the specified items
**cofr**
– the current center of rotation
**camera**
– the viewer position

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).

See also:
command usage conventions

UCSF Resource for Biocomputing, Visualization, and Informatics /
November 2021