What if pdb and dcd do not match?

[Cheng]

I provided the correct dcd file but the wrong pdb file, i.e. the dcd frame does not have the same atoms as the pdb.

However, the command below still works. xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=ca.inds$xyz, mobile.inds=ca.inds$xyz)

May I suggest, if the algorithm can be improved, that all the code can only work when dcd and pdb have the same number of atoms?

[Barry Grant]

Thanks for the note.

We don't force any correspondence between PDB and DCD (or any other input). For the fitting (via fit.xyz()) as long as the fixed and mobile indices are the same length and present then everything should work without an error message. I like having this flexibility.

Perhaps in a future wrapper function specifically for trajectories we might be able to do some basic checking based on total number of atoms but not in fit.xyz() the way it is currently implemented.

[Barry Grant]

Not a bug but a feature request and not addressable currently