Open jadolfbr opened 8 months ago
I had a complex of A B C D. I tried designing specific residues in chain D (like submit_example_4_non_fixed.sh
). Given your post, I tried out the following
I found that the residues of the two experiments were very similar, suggesting that the program is accounting for the other chains.
In the examples, one gives 'design chains' to ProteinMPNN. However, when you give specific positions to design or not design, this gets odd.
For example, if I have a complex of A B C, and I'm designing chain B. I give chain B and a set of non-fixed residues. However, the design of chain B does not take into account A and C. IE design chains is something more to do with masking. If I give A B C, then MPNN takes A and C into account when designing chain B.
I think this is a bit counter intuitive - perhaps some updates in the docs/examples would be welcome here.