What do the `Alignment sequence not found in PDB file or `Number of residues in the alignment and pdb files are different errors mean?
When you give MODELLER an alignment, it also needs to read the structure of the known proteins (templates) from PDB files. In order to correctly match coordinates to the residues specified in the alignment, the sequences in the PDB file and the alignment file must be the same (although obviously you can add gap or chain break characters to your alignment). If they are not, you see this error. (Note that MODELLER takes the PDB sequence from the ATOM and HETATM PDB records, not the SEQRES records.) You should also check the header of your alignment file, to make sure that you are reading the correct chain and residue numbers from your PDB. To see the sequence that MODELLER reads from the PDB file ‘1BY8.pdb’, use this short script to produce a ‘1BY8.
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