Fix robustness issues

[kephale]

copick-usage needs to be improved.

2 issues I've run into so far:

• When looping over pickable objects, always check if they are particles before using them (e.g. using radius).
• When looping over pickable objects, check if a pdb id exists before trying to use.

[uermel]

PickableObject has a mandatory attribute is_particle that should contain this information.

[kephale]

I have a fix I'm using in the notebooks now that I'll submit as a PR once I'm done with the notebooks. It has some other fixes as well.