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Tool: Map Coordinates

The Map Coordinates tool specifies the relationship between volume data grid indices and Cartesian coordinates. This information is included in the header when a map is saved. See also: Volume Viewer, volume operations, getcrd, measurements

Map Coordinates can be started from the Volume Data section of the Tools menu (more...).

The Map of interest should be chosen from the pulldown menu of open volume data models.

Origin index – space-separated grid indices of the XYZ origin (Cartesian 0,0,0). Fractional and negative values are allowed, as the origin is not required to coincide with a grid point or even to fall within the grid. Clicking center moves the XYZ origin to the center of the grid, whereas clicking reset restores the original values.

Voxel size – grid spacing (resolution). Although only one number will be shown if the size is the same along the three axes, three different numbers separated by spaces can be entered. Clicking reset restores the initial values.

Cell angles – angle(s) in degrees between the crystallographic axes

Rotation axis and angle describe a transformation. When a data set is created by resampling, these fields show its transformation relative to the original data set.

UCSF Resource for Biocomputing, Visualization, and Informatics / July 2019