I'm not a big fan of restraining chiral volumes, except for models based
on low resolution data (maybe up to 2.7A). In my experience, if a refinement
results in the flipping of a chiral center the true solution is almost never
to flip it back. If a CA flips then probably a neighboring peptide bond
needs to be flipped. If a threonine CB flips then the OG1 and CG2 labels
need to be swapped.
I would prefer a visual indicator on the screen when a chiral center is
bad in addition to your tool for jumping directly to bad centers. That
way, when I'm passing down the chain I would see, say, an icon with a
picture of a hand with a red circle and diagonal slash and know immediately
that there is a problem. Of course I would also like to see visually the
bad bond lengths and angles, but marking the bad chiral centers would not
clutter the screen and be a good start.
Dale Tronrud
Paul Emsley wrote:
On Tue, 2007-03-20 at 08:57 +0100, Laurent Maveyraud wrote:
Dear list,
another question related to stereochemistry, but concerning coot.
When using the RSR zone button, which should "improve geometry and fit to
map", it seems that the geometry is not always improved : some chiral
centers can be inverted.
That is not always a bad thing.
The surprising thing is that using the "regularize
zone" afterwards does not correct this, even if the chirality of the center
is not set to both, but to positive in the cif dictionary (ie should define
only one possible chirality).
Has anybody else notices this behavior ? Is there a way to adjust the weight
between geometry and map terms in the RSR option ?
Chiral volumes are not part of the geometric target function in Coot[1],
so changing the weight will have no effect.
Currently what I do for chiral volumes (as a work-around) is use
Validate -> Incorrect Chiral Volumes to find the building errors. They
are trivial to fix when you know where they are. Often I use single
atom drag to move the chiral centre to the other side of the chiral
plane (made by the chiral neighbours).
Paul.
[1] They should be, I tried it but it made the minimization slow and
unstable. I should try it again.
