Hello Santhosh--
>
> We are trying to refine an ensemble against RDC and NOE data. The ensemble
> size for now is 2. While going through the examples in eginput/gb3_ensemble,
> I have a few questions.
>
> 1). In the script provided, the starting structure for all the ensemble
> members is provided with command("coor @gb3_refined_IV.pdb"). It means the
> starting structure for all the ensemble members is gb3_refined_IV.pdb. Is
> there any way we could mention different starting structures to different
> ensemble members?
Sure. Bringing things up-to-date somewhat, you would replace lines in
this sequence:
command("coor @gb3_refined_IV.pdb")
esim = EnsembleSimulation("ensemble",ensembleSize)
with (for three initial structures):
esim = EnsembleSimulation("ensemble",ensembleSize)
memberIndex = esim.member().memberIndex()
protocol.initCoords(["file1.pdb",
"file2.pdb",
"file3.pdb"][memberIndex%3]
>
> 2). The aveType : Since we are doing ensemble refinements, the default
> aveType for NOE's and RDC's should be "ave" but I found a few places where
> "sum" is used. What would be the effect of it? Can you help me understand the
> difference between Ave and Sum?
>
These averaging types correspond to averaging within a particular
ensemble member over ambiguous restraints. Averaging observables over
the ensemble is a weighted average (recently, we added the ability to
optimize ensemble weights). I hope this clarifies things somewhat.
best regards--
Charles
_______________________________________________
Xplor-nih mailing list
Xplor-nih@cake.cit.nih.gov
http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
