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John Bruning wrote:
Hi,
Does anyone know of any programs which will fix ramachandran outliers in
an auotmated way without having to do manual rebuilding?
For refining a structure against X-ray data, I think Ramachandran outliers
deserve individual examination. If a residue has refined to an outlier
position then maybe:
-it really is an oulier (in which case you don't want to fix it)
-it was modelled in the wrong pep-flip, rotamer or cis-trans peptide
-the xray data is not strong enough to define the conformation
The most obvious automatic fix would be to move each outlier to the
closest allowed position in phi-psi space. This is pointless because
the two positions will generally be within radius-of-convergence of
each other. As soon as you refine, they will return to outlier
positions. And you don't want to submit an unrefined structure!
You could re-solve your protein with arp/warp if resolution is high
enough, or rebuild the side chains with gui-side if not; refine
that structure and, if the residue is no longer an outlier after
refinement, adopt that rotamer for your structure. But I think it
might be faster to manually cycle through a library of rotamers
(and try both pep-flip), select all that appear possible, and
refine starting from there.
If you are optimizing a model with no x-ray data, the answer is
different. I'm not familiar with these procedures, but I presume
the optimization program penalizes ramachandran outliers, or at
least intrs-residue close contacts, which should result in the
same thing.
Ed
