[modeller_usage] breaking the chain

[M <>]

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*