Hello Liu--
>
> I'm trying to calculate an ensemble of a two domain protein using
> PRE data, and there are two problems now.
>
> The first one is how the final R2 value calculated from the
> contribution of the ensemble members. A similar question has been
> asked in June 2014. The relative answer is pasted below for
> convenience:
>
> "When using sbmf and fast ensInterconvert, there isn't a straight
> averaging over pre contribution, but rather averaging over order
> parameter and distance is done all in one go."
>
> But I don't know how the order parameter was derived. And if
> possible, could you please give a direct function to show the
> average pre calculation?
>
The expressions for calculating the PRE are given in Eq. 10 of
J. Am. Chem. Soc. 126, 5879-5896 (2004). The expressions for order
parameter are given on the same page.
> The second question is how to set different weight for different
> ensemble member. The default weights for ensemble members seem to be
> equivalent. The 'ensWeights' module might help, but I don't know
> the syntax. Could you give me an example script?
>
If you are using an EnsembleSimulation to represent the ensemble, you
can use the setWeights() method of the EnsembleSimulation
object. i.e. if you have a two-member ensemble you would have
ens = EnsembleSimulation('ens',2)
ens.setWeights([0.3,0.7])
to set the ensemble member weight populations.
best regards--
Charles
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