Particle Trajectory Format

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:

Field Changes

Conventionsmust be "CCD"
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

New Fields

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

UCSF Computer Graphics Laboratory / June 2010