> It does work in ARIA 2.3 with analysis 2.1.5 and you can control what goes
> back into the project to some extent. My personal recommendation is to export
> restraints and violations from the final iteration, but not peak lists (can
> mangle your assignments if you're not careful)
My preferred way of working is also to not use ARIA assigned peak lists,
but rather to add to assignments as the structure improves using the NOE
Contributions system, seeding assignments for the solid parts and letting
ARIA figure out the rest.
However, I wish to make it crystal clear that the ARIA export to CCPN does
not overwrite or change any existing peak lists or resonance assignments.
Brian, can you please explain a bit more about what you mean by the
"mangle" comment. Is there something that needs changing?
I do know that the peak lists that come back might have strangely paired
protons and hetero atoms, but the extent of the issue is in the new peak
list and is easily deleted.
> or structures (don't have fine enough control about how many go back and
> from which iteration leading to project bloat).
To be clear, you can use ARIA to export the last iteration and water
refinement structure ensembles. You can also delete old structures. This
keeps the bloat to a minimum.
> The slickest way to get structures in again is to make the ones you want
> (lowest energy selection from final iteration or refinement) into a
> multimodel pdb file (I find the old aqua joinpdb file script handy for
> this) and import through the structures popup in analysis.
You can select and load multiple PDB files in analysis and [Merge Into
Ensemble] rather than use external scripts.
Also, I would say that subjectively selecting PDB files from an ensemble
is not for the uninitiated. Certainly structure calculations can go awry,
to the point where they are not so useful, but also this can be minimised
by gentler MD annealing. I would say that pruning an ensemble can be
dangerous in early calculations because of the risk of biasing toward one
conformation. And in general I think it is better to focus on getting
the interpretation of the NMR data correct, and let the ensemble reflect
the precision in the data.
Personally I like to see some outliers because it gives me more
information about potential problems in the assignment.
T.
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Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766018 (office)
80 Tennis Court Road +44 7816 338275 (mobile)
Old Addenbrooke's Site +44 1223 364613 (home)
Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
United Kingdom http://www.ccpn.ac.uk
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