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Trajectories, Model Series, Volume Series

A trajectory is an ordered series of atomic coordinate sets, or “frames,” opened as a single model. Although the coordinate sets are in a specific order, the data need not be a time series; for example, it could be an ensemble for which the order is not meaningful. Only one frame of a trajectory is shown at a time. Different frames can be shown or played back sequentially with the coordset command, or interactively with a slider interface. A multi-model file in mmCIF or PDB format can be opened as a trajectory by using the command open with coordsets true (default false). A trajectory can also be read from any of several trajectory formats or created with the morph command, and saved to a file with save. The number of coordinate sets in a trajectory can be reported with the command info. See also: crosslinks histogram

A model series is an ordered series of models. A model series can be played back with the mseries command or the associated slider interface.

A volume series is an ordered series of volume data sets (maps). The maps in a single series must be of the same size (number of grid points in each dimension). Volume data can be opened as a series with open, employing filename wildcard symbols or globbing as needed to specify multiple files in a single command; 3D TIFF images and Chimera map files containing five or more same-sized maps are automatically treated as series, if possible, whereas other sets of same-sized maps can be designated as series with the vseries option of open. Volume series can be played back with the vseries command or the associated slider interface.


UCSF Resource for Biocomputing, Visualization, and Informatics / July 2017