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Kortemme-Lab / flex_ddG_tutorial

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Small bug in StoredResidueSubset?? #23

Open frank-stonybrook opened 2 years ago

frank-stonybrook commented 2 years ago

Dear FlexddG developers,

I read through the ddG-backrub.xml script and encounter this line that looks suspicious to me:

<PrimarySequenceNeighborhood name="bubble_adjacent" selector="bubble" lower="1" upper="1"/
<StoredResidueSubset name="restore_neighbor_shell" subset_name="neighbor_shell"/>

where is this neighbor_shell subset being defined in the script? Shouldn't be the bubble_adjacent?

Thanks Cong

frank-stonybrook commented 2 years ago

Any insights on this?

kylebarlow commented 2 years ago

Hi - the logic is a bit confusing, as the neighbor_shell subset isn't initialized until later when the protocol is running by the similarly named StoreResidueSubset mover, which uses the bubble_adjacent selector defined above in the residue selectors definition section. It's been a few years since a put all that together, so if that still seems wrong you probably know more than me, so please let me know.