Re: [modeller_usage] Spatial restraints as "flat bottom" potential

[Modeller Caretaker <modeller-care@salilab.org>]

Esben Jannik Bjerrum wrote:
> 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.
Modeller will try to satisfy both restraints. Since they are 
contradictory, most likely it will end up satisfying one or the other, 
unless they are closely balanced.
> 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?
Sure, but you will need to edit your restraints file. Remove the 6A 
restraint, and the 8A one, and replace them with a flat bottom 
potential, which you can construct with an upper bound harmonic acting 
above 8A, and a lower bound acting below 6A. If the form of this 
potential is not correct for you, Modeller supports arbitrarily complex 
potential surfaces, using cubic splines. See table 3.3 in the manual for 
more information, at http://salilab.org/modeller/manual/node156.html#20884
> Due to glibc compat. errors i've used mod6v2 and not the newest 8v0.
The problem here appears to be an incompatibility with the glibc in 
Debian Sarge. It has been reported to me that the problem goes away if 
Modeller is provided with the glibc from a RedHat 9 box (see the 
instructions in the mod8v0 shell script for instructions). I will 
investigate the issue here, and keep the list updated.
	Ben Webb, Modeller Caretaker
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