Clarify 'design chains'

[jadolfbr]

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.

[proteins247]

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

• Designing D, with specific residues in D specified for design
• Designing A B C D, but only with the same specific residues in D specified for design

I found that the residues of the two experiments were very similar, suggesting that the program is accounting for the other chains.