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

[Modeller Caretaker <>]

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
-- 
             https://salilab.org/modeller/
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