On 5/7/12 7:35 AM, EGY wrote: > Sorry, my question is much more elementary.
Your original question was addressed just last week on the mailing list: http://salilab.org/archives/modeller_usage/2012/msg00152.html
> I see an example from the tutorial (Advanced Modeling, Modeling > ligands in the binding site) on an alignment similar to what I want. > However, I don't see the associated script to give this alignment
You make the alignment yourself, e.g. in a text editor. There is no script to generate it for you automatically.
> In this example, only the binding pocket of the 1emd structure was > included in the alignment. I would also need to know how not to > include a region in one of the other sequences.
Either edit the PDB file to remove the region you don't want to include, or see http://salilab.org/modeller/9.10/FAQ.html#2
Ben Webb, Modeller Caretaker