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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