Thank you very much for your reply.
>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.
Yes, that is correct. But would I also add a chain break character between "b" and "d" in the template?
>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.)
I am modelling a homopentamer. "aaaaabbbbb[ccccc]dddddeeeee" is the sequence for the monomer making up the template, and "fffffggggghhhhh[iiiii]jjjjj" is for a monomer of the target (which is also a pentamer). The .ali file is currently of the form:
>P1;target sequence:target::A::E:::: fffffggggghhhhhjjjjj/fffffggggghhhhhjjjjj/fffffggggghhhhhjjjjj/fffffggggghhhhhjjjjj/fffffggggghhhhhjjjjj*
>P1;template structureX:Mus-5HT3RA-2-clean::A::E:::: aaaaabbbbbdddddeeeee/aaaaabbbbbdddddeeeee/aaaaabbbbbdddddeeeee/aaaaabbbbbdddddeeeee/aaaaabbbbbdddddeeeee*
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?
I look forward to your advice.