On 6/27/2018 3:39 PM, Geoffrey Hutchison wrote:
OB includes an algorithm to perceive bond orders, but it's hardly foolproof. So if you want to ensure bond orders are preserved, don't use those formats.
With PDB, you could convert to mmCIF using either pdb-extract online or download maxit from RCSB. That will calculate the bonds from 3D coordinates and put them in _chem_comp_bond table. Of course doing that that would be a bit back-asswards if you're starting from a format that has correct bond information in the first place.
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