Re: [modeller_usage] Sequence difference between alignment and pdb:

On 9/29/20 3:38 AM, Arnau PC wrote: > as it is a local alignment, there are multiple positions  in the pdb > file that have been skipped in the alignment so I have to remove those > atoms from the pdb file one by one. Additionally, there are missing > positions in the crystal template so I have to remake the alignment > (deleting from the template fasta file these residues) each time I find > missing atoms in the pdb

Right, the sequence in your alignment has to match that in the PDB file exactly, as that's what Modeller uses to map template structural information onto your model. If you don't want to use a template residue in your model, align it with a gap residue "-" in the model sequence.

Ben Webb, Modeller Caretaker