Re: [modeller_usage] Modeling muli-chain protein

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 4/18/14, 12:28 PM, Richard W. Harper wrote:
> Attached is a python script to build a model from the sequence PfFT on
> the template 1JCS.  The first residue in 1JCS is numbered 55.  For the
> start residue in chain A of 1JCS nothing less than 55 is accepted.

What else would you be putting in there? You can't tell it to read a 
residue that doesn't exist from the PDB file.

> However, if I put in 55, it tries to align residue 55 in the pir
> alignment file with residue 1 in the sequence.

You mean residue 55 in your template is aligned with residue 1 in your 
model? Modeller doesn't "try to align" anything - your alignment file 
defines what is aligned with what. If you want a 54-residue insertion at 
the start of the model, you'd need to put that in your alignment.

	Ben Webb, Modeller Caretaker
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