Re: [modeller_usage] sequence file produced is different from the one shown in the tutorial

On 9/21/12 1:26 PM, Sajeewa Pemasinghe wrote: > In the field 5, it says +238 whereas in the tutorial, in the resulting > 1qg8.seq file it shows 256. Have I done any mistake? Would the above > sequence file work just as fine as the one shown in the tutorial?

The PIR alignment format is described at http://salilab.org/modeller/9.11/manual/node476.html

"+238" means "read 238 residues from the PDB file". "256" means "read until you reach the residue numbered "256" in the PDB file".

They should both result in the same thing. I suggest you run it and see.

Ben Webb, Modeller Caretaker