the position of the N-terminal of the binder

[july591]

hi, on what basis is the position of the N-terminal of the binder generated by bindcraft determined? The N-terminal of the generated binder is in a fixed position, but this is the opposite of where I want the sequence to be. How do I adjust this position?

[martinpacesa]

Not quite sure what you mean, can you give an example?

[july591]

Not quite sure what you mean, can you give an example?
As an example with this protein, the red part in the middle is the generated binder. What I want is for the N-terminus and C-terminus to be positioned like this, with the N-terminus at the bottom and the C-terminus at the top.

but, the generated structure is the opposite of what I want, like this：

[martinpacesa]

Hmm, so currently there is no way to do that, but I suppose you could write a custom loss function to keep the N terminus as far away from the target as possible

[july591]

Hmm, so currently there is no way to do that, but I suppose you could write a custom loss function to keep the N terminus as far away from the target as possible

Thank you for your reply