Hi Manuel,
Recently I have been using the RDKit Open3D alignment method via the python bindings (in IPython notebook), and it occured to me that I could/should test the same within KNIME using the RDKit nodes.
One option that Paolo just explained to me (when I bumped into him at the UKQSAR meeting yesterday) was the 'local optimisation' setting. At the moment this is not exposed in the KNIME interface, but I thought an additional checkbox doing so would be useful for others as well(?). [implementation detail: if checked, this woul just add 4 to the selected accuracy level - to give the final options int]
Just to put it in context a bit - what I am looking at is taking two overlayed ligand-bound structures (same protein, different ligands) and I wanted the MMFF atom typing and partial charges for the two ligands to dictate which 'important' atoms I could then look at RMSD values for (please don't scrutinise the idea too much - it is a work in progress!). Anyway, the problem was that the Open3D alignment would try to give the 'best' global alignment, and what I want is a 'close' local alignment.
One other thing I have just noticed with the RDKit node - the aligned molecule doesn't seem to have hydrogen atoms even if they were explicitly present in the input molecule! I'm sure I could add them - but I guess I wouldn't expect to need to, as they were present in the input... From memory some others of the RDKit nodes also seem to strip explicit hydrogens, but I need to remind myself which.
Kind regards
James