[buster-discuss] special position in refine v1.10.0
osmart at globalphasing.com
Fri Feb 3 18:40:28 CET 2012
On Fri, 3 Feb 2012, Dale Tronrud wrote:
> I agree with Peitro. I don't know of a reason why an atom must be exactly
> on the symmetry axis. Often the density on the axis is not spherical so either
> you have anisotropic B's (for a small deviation) or the atom has to shift a
> bit off center.
> If a bad contact restraint is pushing the atom away, then the EXCLUDE
> statement should do the trick.
> Dale Tronrud
It can be a reasonable choice to model an atom or ion on a special
position with a single atom that lies exactly on axis or position.
I think that SHELX allows this to be done with constraints. I would
like to allow BUSTER users to choose this with the distance restraints
If the atom is allowed to drift from axis then it is a bit like allowing
two alternates on a "normal" water. It is a perfectly reasonable modelling
choice. But additional refinement parameters are introduced by allowing
the atom to move off axis. In my limited experience density on symmetry
axes is difficult to interpret and can have artefacts.
The special position handling in BUSTER is not yet completely sorted. The
current state-of-play is described:
The distance cut-off used does mean that drift can suddenly mean fully
non-bonded terms appear and the atom flys away from the axis.
| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK |
| http://www.globalphasing.com/people/osmart/ |
More information about the buster-discuss