ValueError: The number of FASTA sequences does not match the number of chains

[kexul]

Hi, I tried to prepare the system for protein '4E4N' and encountered this error: ValueError: The number of FASTA sequences does not match the number of chains.

Here is the minimum code to reproduce that:

with Dir('SYSTEM', overwrite=True):
        # create a protein from its PDB code and the residue number of the ligand
        # we are going to use for mapping
        protein_proto = Protein('4e4n', ligand_ref='1201')

Any help is appreciated!

[kexul]

It seems like that the protein 4E4N is a dimer. I've checked the protocaller paper's supplement files, which have dimer '6DAV' as an example, but the code used to prepare the system shows that it remove the chain after download the protein from pdbbank. So the error should be related with the updated version of protocaller I think.

protein_B = Protein("6DAV", ligand_ref=ligands["reference"], workdir="6DAV_B")

for chain in protein_B.pdb_obj:
    for residue in chain:
        atoms_to_purge = [x for x in residue if x.altLoc == "A"]
        residue.purgeAtoms(atoms_to_purge, "discard")
protein_B.pdb_obj.writePDB()

[msuruzhon]

This was an issue of the FASTA file only containing one sequence for the two chains. I wrote a thin wrapper that detects when this is the case and copies the sequences. 4E4N works now in my tests. Feel free to reopen if there are problems with some other proteins, since I am not sure how general this solution is.

[kexul]

Hi @msuruzhon , here is another protein '2QJR' raised the same error.