On 05/29/2012 06:58 AM, M wrote: > I don't want to model one fragment of a protein. I want to achieve > this by using the "" sign in the alignment, but I'm not sure how the > pir file should look after insertion of the "" sign. Should it look > like this:
You're close, but you need to make two changes:
1. It's the '/' sign, not the ''.
2. Since a chain break denotes a break *between* two residues, it has zero width. It doesn't make sense to align a chain break with a 'real' residue; you need to align it with either another chain break or a gap. So in this case you probably want to add a gap to your template:
>P1;template structureX: (...) ABCDEFGH-JKLMNOPQRSTUVWXYZ*
>P1;target sequence: (...) ABCDEFGH/-------QRSTUVWXYZ*
Note also that your example alignments are not valid PIR format; each sequence must start with >P1; as above, not <P1 or <P2.
Ben Webb, Modeller Caretaker