[modeller_usage] Spatial restraints as "flat bottom" potential

[Esben Jannik Bjerrum <>]

I'm trying to model a flexible protein where two highly rigid domains
move in respect to each other, and would like to model some of the
states between the two extremes in the templates. 
When I model with the open and closed form of the protein as templates,
I only get open and closed forms af the target. As I initially
understood the spatial restraints, they are an average of the
restraints extracted from the templates. But it seems to me now, that
when theres a spatial restraint of f.ex 6Å from one template and 8Å
from the other, modeller tries to match either 6Å or 8Å in the target,
where 7Å is not OK. Please correct me if I misunderstood.
Is it possible to change this behaivor to a flat bottom potential? To
take the former example: So that any distance in the range 6-8Å is
equal, and the potiential then rising outside that?
Due to glibc compat. errors i've used mod6v2 and not the newest 8v0.

Best Regards
Esben Jannik Bjerrum


		
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