Hi Paul,
Am 14.04.11 15:03, schrieb Paul Emsley:
Let's be clear what you mean, do I understand correctly?
You are refining one residue and you want that residue to know about
it's environment - i.e. residues that have not been selected for
refinement and won't move, but will influence the refinement because
they can provide vdW or H-bond restraints to the moving atoms?
yes, that's exactly what I want, but only if I'm convinced that the
fixed environment atoms are (more or less) in correct positions.
Otherwise, I would prefer to ignore them, because they might give false
VDW repulsions or false H-bonds attractions.
You can do something like that with sphere refinement - and fixing the
atoms that you don't want to move.
Understanding hydrogen bonds in refinement though is not something
that coot does at the moment. Some of the underlying code has been
written but this feature is not available yet. It will be - keep
poking :-)
I'm looking forward to this :-)
Best regards,
Dirk.
Paul.
On 14/04/11 10:37, Dirk Kostrewa wrote:
Another idea, that I propose from time to time, would be to have a
complete force-field like geometry term, including VDW repulsions and
hydrogen bonds. This would avoid refining atoms into already occupied
places and it would maintain secondary structures even at very low
resolution.
Best regards,
Dirk.
Am 14.04.11 11:32, schrieb Bernhard Lohkamp:
This is an idea I had for a while but never had the time to implement
or test (it's still on my list though). For now torsion angle
refinement and especially back-rub rotamer fitting of side chains
(default for lower resolution; 2.8A IIRC) should help to prevent side
chains from moving into the 'main' density.
B
this one is for Paul, but maybe it's worth discussing it on the list.
If that
feature already exists, please let me know.
Would it make sense to down-weight the side chain atoms in real space
refinement? At low resolution I often find that the side chain atoms
are dragged
into the density of where I suspect the main chain to run, and maybe
this effect
could be avoided by downweighting the X-ray 'force' on the side chain
atoms.
This might correspond to having different matrix values for main and
side chain
atoms.
I am curious to hear comments about this idea.
Cheers, Tim
--
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
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D-81377 Munich
Germany
Phone: +49-89-2180-76845
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