Hi all,
I am trying to find the orientation of a small "flanking
domain" with respect to the main body of the protein (the
core) by molecular replacement in CNS. I already have the
core positioned correctly but the flanking domain is
flexible and moves vis-a-vis the core between my model and
my structure.
The question is, is there a way to do a cross-rotation
search for just the flanking domain, with the core 'fixed'
in place? When I do a patterson search with just the
flanking domain, there are no significant hits, which makes
sense because the flanking domain is only 25% of the
protein. If there was a way to treat the core and the
flanking domain as two rigid bodies during the
cross-rotation search, this would work exceedingly well. Has
anyone encountered this problem before and is there a way of
attacking it? Any help would be greatly appreciated. Thaks
in advance!
d'pesh
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