On 3/12/24 11:14 AM, hmad3--- via modeller_usage wrote: > If I remove "iiiii" from the sequence before aligning with the above > template sequence (without the disordered region), "h" and "j" will > be interpreted as continuous in the .pdb file of the target > generated, affecting the structure of the protein. How would I make > PDB interpret a gap between "h" and "j" that aligns with the gap > between "b" and "d" in the template?
I think by "gap" here you mean "chain break", i.e. you don't want a peptide bond between the last residue in "h" and the first residue in "j". This is straightforward: add a chain break character ("/") between h and j in your target sequence. This simply tells Modeller to not construct that peptide bond. Normally one would align a chain break in the target with a chain break or a gap ("-") in the template.
> Another note: both the template and target sequences are single chains.
Perhaps you mean all residues have the same chain ID. The target will be two chains if you add a chain break. (Modeller will by default label them A and B, but you can call them both A if you like.)
Ben Webb, Modeller Caretaker