[modeller_usage] Re: I don't want to use one region of a *target* for construction of my model.

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.