Sorry, my question is much more elementary. 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, only the resulting pap file. 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. Thanks. On May 7, 2012, at 9:43 AM, Thomas Evangelidis wrote: Also allow for some overlap to ensure loop closure. I.e. |