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Have you solved this issue with PDB-format structures? I have only PDBs as well. Notice that the authors said they provided two scripts to process the structures, but only rcsb.py was contained. It is likely that another script could process the PDBs. And the msa_id should be corresponded with the related chain.
If I only have the pdb file, how to perform the 7-th step of "Processing raw data".
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