always get mistaken chain connection in binder design

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
python
Domain
bioinformatics, machine-learning

Research direction

Start by reproducing the binder-design setup shown in the issue and inspect how the /0 chain-break marker is interpreted for chains E and F. Compare the original and diffused structures, then determine whether the unselected regions retain their intended connections; done means chain breaks and undeclared regions are handled correctly.

Written by the indexing model from the issue text.

Description

image
here shows the partial comparison between original stucture and the one after diffusion. confusingly, i always get wrong connection within those part that i did not declare to be disigned.
image
i use /0 as the sign for chain break but seem to be failed, since chain E and F was connected wrong

i havent figure out the exact rule behind, any advice will be appreciated!

Dominant language
Python
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