nbehrnd

Applying the same pattern as for the small molecule example ```bash $ obabel P04406.mmcif -O probe.sdf ============================== *** Open Babel Warning in PerceiveBondOrders Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders...

@multimeric I gave the data file a second chance for the couple of [Jmol](http://jmol.sourceforge.net/) and OpenBabel. For one, the conversion into individual molecules works much better (a Zn, a large...

I read your lines in the tune of «nice that Jmol is able to contribute to a solution, but it does so only via a GUI». If this interpretation were...

From the perspective of small molecules: Does `diff` reveal differences on these hydrogens only? Do the heavy atoms (CNOPS) move a little, too? If these structures are not too big...

For what applications are these numerical fluctuations of chemical relevance for you? Since I do not see OpenBabel as a replacement for a program dedicated to computation as in quantum...

Your request to openbabel `--gen3d` launches a minimization to identify one optimum (it need not be the the global one). Some cases are more difficult than others; check if the...

I'm not sure if this is possible as an output format. Do you want to base your query on PubChem's chemical identifier (CID)? From a previous case, I recall passing...

This is more a commentary to improve the presentation of your question, than as to provide a solution: + Update openbabel. With version 2.4.1 you mention, you limit your work...

@fredrikw Good point to spot the missing H in the first structure _as if_ the structures might be subject to keto-enol tautomerism. In fact, submitting the SMILES assigned by ChemDraw...

Is the same problem observed if you upgrade your OS to a more recent version (e.g., substitute 16.04 by 20.04LTS, if not 21.04) and then resolve the dependencies from the...