>I've seen this happening to water molecules as well (in a somewhat
>unpredictable fashion). In the latest refmac versions, you can try
>harmonic restraints, although these will only slow down the atom drift,
>as the target position is updated every cycle.
>
>Perhaps you can use distance restraints against a dummy atom to fix the
>metal ion in place.
Thanks, Ed!
Just in case anyone else has the same issue:
With Garib's help, I have forced the atom into its position by using
external distance restrains of zero length against the same
symmetry-related atom. The cause is unclear because the same program
handles special positions in another structure just fine. Here is the exact
command I used:
EXTERNAL DISTANCE first chain M residue 3 atom MN -
second chain M residue 3 atom MN value 0.0 sigma 0.00 symm Y
Occupancy set manually to 0.5.
- Dima
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