Hi all,
I am trying to refine a crystall structure with one set of RDCs. In
this refinement, I need to apply position restraints to keep the whole
protein folded correctly. What I do was keep the the backbone atoms of the
residues which have secondary structures in the postion of the original
structure. The position restraints are applied as below:
"
from posDiffPotTools import create_PosDiffPot
refRMSD = create_PosDiffPot("refRMSD",
"(resid 2:7 or resid 10:16 or resid 23:34 or
resid 38:44 or resid 56:59 or resid 66:71) and (name CA or name N or name
C)",
pdbFile="ubnmr.pdb")
refRMSD.setUpperBound(0)
refRMSD.setScale(10000)
potList.append(refRMSD)
"
After the refinement, most secondary structure folded correctly. But
several B strands do not folded well. I want to applied higher energy just
on these residues which do not folded well. Thus I need to setup two set of
position restraints like above, but with different energy. I do not know how
to do that. Does anyone know how to do that?
Thanks,
Xiaogang
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