Hi Chris,
from what you described I understand that there are two spices in
alternating locations that share the same or nearly the same space.
In this case assign one of them altloc A, and the other one altloc
B. Then define the constrained group constituting these two species
as described here:
http://phenix-online.org/documentation/refinement.htm#anch22
If you do so, their occupancies will be refined, and each species
will end up with a partial occupancy 0<=q<=1, and the sum of
the two group occupancies will add up to one.
Also they will not "see" each other through repulsive restraints
term and therefore will not be pushed apart.
If you have any questions or difficulties to do what I just
described above, then please send me the PDB file and point out the
atoms in question and explain how you want to refine them, and I
will send you back a working example.
Pavel
On 2/27/12 8:11 PM, Christopher Wanty wrote:
Hi,
I have a problem with a phosphate moving out of position
during refinement. The complication is that there is an
existing phosphate in the same location as the one I’m trying
to place, but the existing one is part of a modified residue,
and there is clearly density for the alternative conformation
of the phosphate, but it is also clearly not still bound to
the residue.
How do I make sure that the phosphate does not move away from
where it should be? Attached image show the phosphate more or
less where I want it, and you should be able to see where the
existing phosphate is attached to the residue. The large red
density blob is where phenix.refine tried to put the phosphate
last time.
Kind regards,
Chris
-------------------------------------------------------
Dr. Christopher Wanty
[email protected]
Research Associate
Biomolecular, Biomedical and Chemical Sciences,
Building M310
University of Western Australia
35 Stirling Highway
Crawley 6009
Western Australia
Australia