Hello Diego--
>
> I am trying to pack two long dimeric coiled-coil structural elements
> onto each other using SAXS data to drive the modeling.
> Is there a way to restrain the positions of the center of mass of
> the two coiled-coil elements within a defined distance range?
You can use the NOEPot distance restraint term with center averaging,
The two selections of the restraint would specify the corresponding
structural elements. In this way the distance restrained would be
between centroids, rather than the centers of mass:
from noePotTools import create_NOEPot
dist = create_NOEPot('dist',
restraints="assign (resid 10:20) (resid 90:100) 10 2 3")
dist.setAveType("center")
dist.setScale( 100 _
potList.append(dist)
This would restrain the centroids of residues 10-20 and 90-100 to lie
in the range 8-13 angstroms.
For this problem, however, you may instead wish to use ambiguous
distance restraints to pull the structural elements together. Or
perhaps even a gyration volume term to pack them.
I hope this helps--
Charles
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