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. A trajectory can be played back with the coordset command, the associated slider interface, or the play coordinates mouse mode , and saved to a file with save. If molecular surface calculations make playback slow, it may be necessary to use the surface option update false. See also: making movies

Atomic trajectories can be created by morphing or by opening files from other programs. Details for opening files depend on the file format:

• 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 be read from any of several trajectory coordinate formats by first opening a structure (e.g. from a PDB file) containing the same set of atoms as the trajectory, and then opening the the coordinate file by using open with the structureModel option to specify the already-open atomic structure. The structure is needed to supply the topology, or bonding pattern, as it is not included in the coordinate file.
• If a PSF trajectory topology file is available, however, it can be opened using the menu (File... Open) and the user will be prompted to open the corresponding trajectory coordinate file. A PSF file can also be opened by using open command with the the coords option to specify the trajectory coordinate file.

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. If a volume series is opened by choosing multiple TIFF files in the dialog from menu: File... Open, the sort order in the dialog may define the temporal order. Volume series can be played back with the vseries command, the associated slider interface, or the play map series mouse mode . Markers placed on volume series data are assigned a frame attribute with value indicating the associated time step within the series. See also: volume, measure motion