Add ability to make models that have same hydrogens as final trajectories.

[sonyahanson]

This is to plot 'reference pdbs' onto the same coordinates as trajectory analysis.

So far I have just been using implicit refined models for this, which has worked okay. It would be useful if it is not refined though, since we are using the pdb as a reference structure.

Additionally, if the implicit refined pdb is never made because the simulation crashed or because this structure is not in the database yet, then using the implicit refined structure is not a choice at all. Sometimes this has been the case for a specific structure requested by a collaborator, and we are not able to give them the comparisons that are most useful to them.

[jchodera]

For the hydrogen issue, what if we just sliced out and used heavy atoms in analysis?

The problem of Modeller failing to produce a model is much harder to solve. Are there specific cases where you can look into the logs and extract the Modeller failure logs?