trimPDBEnsemble doesn't work when inputs to buildPDBEnsemble are sele

[jamesmkrieger]

with the following code (from the scipion plugin) applied to some spike structures, we get the following error:

            ens = prody.buildPDBEnsemble([tar.select(self.selstr.get()) for tar in self.tars],
                                          ref=ref,
                                          seqid=self.seqid.get(),
                                          overlap=self.overlap.get(),
                                          match_func=match_func,
                                          atommaps=atommaps)

            ens = prody.trimPDBEnsemble(ens, 1.)

ValueError                                Traceback (most recent call last)
Input In [6], in <module>
----> 1 ens = trimPDBEnsemble(ens, occupancy=1.)

File /mnt/c/Users/james/code/scipion3_new/software/em/ProDy/prody/ensemble/functions.py:281, in trimPDBEnsemble(pdb_ensemble, occupancy, **kwargs)
    279 select = atoms[indices]
    280 trimmed.setAtoms(atoms)
--> 281 trimmed.setAtoms(select)
    283 coords = copy(pdb_ensemble._coords)
    284 if coords is not None:

File /mnt/c/Users/james/code/scipion3_new/software/em/ProDy/prody/ensemble/ensemble.py:265, in Ensemble.setAtoms(self, atoms)
    263     ag = atoms
    264 if ag.numAtoms() != n_atoms:
--> 265     raise ValueError('size mismatch between this ensemble ({0} atoms) and atoms ({1} atoms)'
    266                     .format(n_atoms, ag.numAtoms()))
    267 self._atoms = ag
    268 self._indices, _ = sliceAtoms(self._atoms, atoms)

ValueError: size mismatch between this ensemble (2955 atoms) and atoms (24015 atoms)

I think we need to use getAtomGroup somewhere for generating and/or applying the indices. Perhaps, we could/should also use trimmed.select with a selstr based on them too.

[jamesmkrieger]

This doesn't happen when the reference is an index

[jamesmkrieger]

In fact, a lot of things aren't made to handle that. All the get functions that use indices (getMSA, getCoords, getCoordsets, etc.) have problems and loadEnsemble does too