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:
| Attributes | |
|---|---|
| Conventions | must be "CCD" |
| Dimensions | ||
|---|---|---|
| particle | required | replaces 'atom' |
| molecule | optional | number of molecules
(particles are organized into molecules via the molecule_numbers data variable) |
| connection | optional | number of particle-particle connections |
| Data Variables | ||
|---|---|---|
| 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 |