Well - A and B are meant to be flags to show there are 2 conformations
of a particular unit. sp they arent appropriate here and may be muddling
things up.
On the other hand you shouldnt get any repulsion between pairs of atoms
whose added occupancy is <= to 1.0
Is that always the case for your 2 scenarios?
Try removing the A and B flags and see if that is better.
Eleanor
Stefan Arold wrote:
Dear All,
I am having trouble refining a difficult case of alternate structures
in REFMAC. In the crystal, two states superimpose:
1) Apo-protein with its own auto-inhibitory tail fixed into the ligand
binding site
and
2) Peptide-bound protein, where the peptide has displaced the
auto-inhibitory tail.
this also includes alternate side-chains of the protein ligand binding
site, according to the apo state or peptide-bound state
I was hoping that assigning 'A' and 'B' alternate states (for 'apo'
and 'peptide-bound') to the protein chain (chain A)
[ex:
ATOM 62 C ATYR A 17 20.856 42.150 21.476 0.60
75.23 C]
and state 'B' to the peptide
[ex:
ATOM 87 N BALA D 513 9.910 69.145 50.780 0.40
20.00 N]
would do the job - but unfortunately, even though refmac refines this
structure, the two states 'sense' each other, and refmac refinement
applies repulsive forces, pulling the apo-auto-inhibitory tail and the
peptide away from each other...
Neither the refmac manual, nor the ccp4bb archives helped, so I
thought one of you might...
many thanks
Stefan
