Hello Charles,
This is more of confirmation than anything.
I know that RDCpot is a weighted average, where the weights provided by:
#weights is a list of weights
esim = EnsembleSimulation("ensemble",ensembleSize)
memberIndex = esim.member().memberIndex()
esim.setWeights(weights)
are used for computing the weighted average. Are NOE's too done this way?
It was not mentioned in the documentation.
Is there anything in particular that I should take care when using weights
apart from that one line of code esim.setWeights()?
Thanks for your time and patience,
santhosh
On Fri, Aug 30, 2013 at 9:19 AM, Charles Schwieters
<char...@schwieters.org>wrote:
>
> Hello Santhos--
>
> >
> > While I was going through example scripts, in eginput/gb3_ensemble and
> > comparing against eginput/gb3_rdc [single structure refinements], I found
> > some thing that looks weird.
> >
> > In eginput/gb3_ensemble:
> > dyn = ivm.IVM(esim) #manipulator for T-A dynamics
> > dynx = ivm.IVM(esim) #manipulator for Cartesian dynamics
> >
> > but dynx was never used as a cartesian dynamics [no call to
> > protocol.cartesianTopology(dynx).]
> > Is there a reason to do that? How to perform a cartesian minimization
> when
> > running an ensemble simulation?
>
> These scripts were written before those helper functions existed. They
> are manually setup for T-A and Cartesian dynamics.
>
> >
> > I have tried to mention,
> > protocol.torsionTopology(dyn)
> >
> > protocol.cartesianTopology(dynx)
> >
>
> This must be done carefully, as the IVM objects are already configured...
>
> > but the resulting refinements should some bigger R-factors than ones
> > that did not.
>
> ...as you found out. In particular, the RDC setup has changed to use
> the freedom member instead of manually calling the configIVM
> functions. To use cartesian/torsionTopology you will need lines like
>
> rdc.oTensor.setFreedom("fixDa, fixRh")
>
> instead of the calls to configIVM*. The contents of the string passed
> to setFreedom can be found here:
>
> http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/varTensorTools.html
>
> best regards--
> Charles
>
>
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