On 7/15/14, 5:11 AM, Josh Bullock wrote: > so when i create a rigid body, i'm decorating a selection of particles - > but it's the particles that hold all the information. and what i want to > add to the root hierarchy are the decorated particles, not the decorator > itself, correct ? i think that this is why i was getting no mass before.
A decorator is simply a pointer to a particle. Generally speaking you can use a decorator wherever a particle is expected, and the underlying particle will be automatically extracted.
> so when i load a pdb into IMP, a particle is created for each atom ?
Yes, but also for each residue, chain, and protein.
> rb_mover = IMP.core.RigidBodyMover(m, > IMP.kernel.Particle.get_index(IMP.Particle(m)), maxTranslation, > maxRotation )
Not sure what you're trying to do here. This will create a new empty particle (not a rigid body). RigidBodyMover expects you to pass it an existing rigid body, usually created from an existing hierarchy by means of create_rigid_body().
Ben