Values at Atom Positions Values at Atom Positions icon

Values at Atom Positions maps volume data to atom positions and assigns the values as an atom attribute. See also: Fit in Map, Rotamers, Surface Color, measure mapValues

There are several ways to start Values at Atom Positions, a tool in the Volume Data category (including from the Volume Viewer Tools menu). The Molecule (containing the atoms onto which data values will be mapped) should be chosen from the list of open molecule models. The Volume data should be chosen from the list of open volume data sets. Browse... can be used to locate and open a volume data file.

The attribute will be named value_name, where name is the name of the volume data set (except with any characters other than numbers and letters changed to underscores). For example, an attribute based on the volume data file default.phi will be named value_default_phi.

Values of the attribute are assigned to all atoms in the chosen molecule model. The transformed coordinates of the molecule model and the volume data (but see below) are used to map data values to atoms. For each atom within the bounds of the volume data, the value is found by trilinear interpolation from the eight corners of the enclosing volume grid cell. Atoms outside the bounds of the volume data are assigned a value of zero.

Clicking Histogram assigns the values and opens Render/Select by Attribute, which includes a histogram of the values.

Close dismisses the dialog, and Help opens this manual page in a browser window.


Values not saved in sessions. The new attribute and associated values are not saved in session files.

Volume data must be displayed before it can be transformed separately. There is no volume model until the data is displayed with Volume Viewer. When there is no volume model, the transformation of the volume data is assumed to be the same as that of the chosen molecule model. To use a different transformation for data mapping, the volume data must be displayed and the volume model moved while the molecule model is held fixed (or vice versa).

UCSF Computer Graphics Laboratory / September 2012