On 12/18/2013 03:42 AM, Jurgens de Bruin wrote: > I would like to know what would be the best option to exclude residues > from the N and C terminal of the target. The sequence can be truncated > in the fasta file before modelling I believe would be the easy answer > but does MODDELLER have a option/function that would have this?

If you don't want the residues in the model at all, the only way to do it in Modeller is to remove them from the modeling alignment. You can either do this manually, or programatically using something like alignment.edit(): http://salilab.org/modeller/9.12/manual/node293.html

Ben Webb, Modeller Caretaker