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Hi, Most likely the pdb file contains the CONECT record for bonds only for a few non standard residues or small molecules, so since there are bonds MDAnalysis will not try to guess the missing ones. |
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I get a lot of warning like WARNING: not removing hydrogen atom without neighbors
the protein_file file are from maestro in pdb format
u = mda.Universe(protein_file)
protein_mol = plf.Molecule.from_mda(u)
plf.display_residues(protein_mol)
May I ask why the display function cannot show the residues?
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