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