Trajectories can be viewed and analyzed with MD Movie. The particle trajectory format is intended for coarse-grained systems in which the individual particles are not atoms but higher-order structures such as residues or domains.
In Chimera, the particles are implemented as atoms, particle-molecules as residues, and connections as bonds. This allows use of commands and menu actions much the same as for standard atomic systems. For example, in the command line, @lipid would specify all particles named lipid, and :golgi would specify particles with particle-molecule name golgi.
The format adheres to the Amber Trajectory NetCDF Convention Version 1.0, Revision B, with the following exceptions:
|Conventions||must be "CCD"|
|molecule||optional||number of molecules
(particles are organized into molecules via the molecule_numbers data variable)
|connection||optional||number of particle-particle connections|
|particle_names(particle)||optional||particle names; defaults to "prt"|
|radii(particle) units="angstrom"||optional||particle radii; defaults to 1.0|
|molecule_names(molecule)||optional||list of "molecule names" for groups of particles; defaults to a list containing the single item "PRT"|
|molecule_numbers(particle)||optional||1-based index into the molecule_names list (one entry per particle); defaults to a list containing 1 for each particle|
|connections(connection,2)||optional||pairs of 1-based indices into the particle list, indicating particle-particle connections|