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JeffSHF / ColabDock

Code for ColabDock paper
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Gaps in template structure #7

Closed fabgonzal closed 6 months ago

fabgonzal commented 1 year ago

How are gaps in the template structure treated for numbering purposes? Say I have a chain with residue 40 and 42 modeled but 41 is not. When putting in constraints will everything after the gap be shifted one or will the numbering respect the gap?

JeffSHF commented 1 year ago

Hi. In this case, since residue 41 is not in the pdb file, it will be ignored and residue 42 is numbered as 41. Also, note that residue 41 also does not appear in the final docking structure. So if you want a docking structure without gap, please first fill the gap in the template using rosetta or other tools.