On 3/12/24 3:33 PM, hmad3--- via modeller_usage wrote: >> 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. > > Yes, that is correct. But would I also add a chain break character > between "b" and "d" in the template?
Yes, or a gap, it makes no difference.
> Another note: the template monomer sequence is also missing the first > few N-terminal residues of the precursor protein - i.e. the full > sequence is zzzzzaaaaabbbbbcccccdddddeeeee, with zzzzz and ccccc not > being included in the .pdb file, so that the N-terminal-most "a" is > marked as residue 6, not 1. Likewise, the full target monomer > sequence is yyyyyfffffggggghhhhhiiiiijjjjj, with yyyyy aligning with > zzzzz. I deleted yyyyy, and in the .pdb file for the target, the > N-terminal-most "f" is marked as residue 1. Does it matter - should I > try to make the first "f" marked as residue 6?
You can model whatever target sequence you like. If it's aligned, Modeller will use information from the template; otherwise, it will be modeled using just the CHARMM forcefield. Modeller also doesn't care about the residue numbering; that is just for the human's benefit. If you want a different numbering, use rename_segments() as per https://salilab.org/modeller/10.5/manual/node30.html
Ben Webb, Modeller Caretaker