Hello Hiroki--
> I have been trying the ensemble refinement of a protein‐protein >
> complex with PRE data using XPLOR-NIH 2.34. I could carry out
> the > ensemble refinement under standard condition, and now I’m
> trying the > ensemble refinement with one of the ensemble member
> held fixed, like > Nature (2006) 444, 383 (“The stereospecific
> complex was held fixed > and other 20 ensembles of non-specific
> complex were included in the > simulated annealing docking
> calculations.”), and JACS (2011) 133, > 14176 (“ The converged
> N[e] = 1 complex ( obtained from the single > ensemble
> calculations ) was held fixed and the supplemented N[e] = 3 >
> ensembles were included in the simulated annealing docking >
> calculations. ( N [e] = 1 + 3 ensemble representation) ”).
First, these sorts of calculations are performed by first subtracting
out the contribution of the fixed ensemble member, such that only the
optimized members are explicitly present in the calculation.
Second,if for some reason the full ensemble is needed, the setup would
be:
memberIndex = esim.member().memberIndex()
dyn_fix = IVM(esim)
dyn_fix.group( 'resid 301:376' )
dyn_fix.fix( 'resid 6:234' )
if memberIndex==0:
dyn_fix.fix( 'resid 301:376' )
protocol.torsionTopology(dyn_fix)
[Do note that the call to torsionTopology should be after
other fixing and grouping.]
I apologize for this not being clearer.
best regards-- Charles
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