Hi,
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:
<P1 structureX: (...) ABCDEFGHJKLMNOPQRSTUVWXYZ*
<P2 sequence: (...) ABCDEFGH------QRSTUVWXYZ*
or like this, with additional gap sign:
<P1 structureX: (...) ABCDEFGHJKLMNOPQRSTUVWXYZ*
<P2 sequence: (...) ABCDEFGH-------QRSTUVWXYZ*
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
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Modeller Caretaker