I am using Avogadro for plain simple visualisation of molecules and SMARTS queries for specific structures.
After some odd results, I thought that I was coming up to some form of a bug within openbabel, but that turned out not to be the case. This whole investigation however revealed that there might be some discrepancies within the PDB files.
I have noticed that these discrepancies do not seem to affect Avogadro (?). If I select a fragmented residue, it is still rendered as a connected sub-structure.
Can I please ask how does Avogadro handle these missing bonds? Is there a systematic way of inferring them?
All the best