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3D-Beacons / 3d-beacons-client

Implementation of the 3D-Beacons client (local 3D model server)
Apache License 2.0
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PDB to mmCIF converted files do not validate for the PDBx/mmCIF dictionary #31

Open bienchen opened 2 years ago

bienchen commented 2 years ago

The mmCIF files converted from PDB input to not validate against the PDBx/mmCIF dictionary. They are missing some essential categories. Raised the issue also with Gemmi: https://github.com/project-gemmi/gemmi/issues/178

Output of CifCheck:

ERROR - In block "P38398_1jm7.1.A_1_103", parent category "entity_poly_seq", of category "atom_site", is missing.
++ERROR - In block "P38398_1jm7.1.A_1_103", parent category "pdbx_poly_seq_scheme", of category "atom_site", is missing.

entity_poly_seq appears when gemmi convert is invoked using -s. But then entity_poly is still missing.