Thanks to Eleanor and Boaz for their quick reply;
Here some additional infos:
I am using ccp4 6.0; Refmac_5.2.0019 version 5.2.0019
and the data are only to about 2.8 A
I have tried to leave out the alternate flags - still the same: the
repulsion persists...
I have also tried to use the same chain label for the peptide and the
protein (to simulate two conformations of a pseudo-hybrid unit), but
this didn't help either...
best wishes
Stefan
Eleanor Dodson a écrit :
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
--
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Stefan T. Arold, PhD
Centre de Biochimie Structurale
CNRS UMR 5048 - UM 1 - INSERM UMR 554
29 rue de Navacelles 34090
MONTPELLIER Cedex - France
email: [EMAIL PROTECTED]
Phone: +33 (0)4.67.41.77.02
Fax: +33 (0)4.67.41.79.13
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