Hi Joel,
I'm working on a similar structure at the moment.
If refining in refmac, you could add a line to the pdb such as:
LINKRSG ACYS A 22 SG ACYS A 96SS
and tell the program to only use links defined in the pdb file.
If refining in phenix, you could set the parameter for the disulfide
distance cutoff from 3.0 to 2.4 A so that the automatic detection only
finds the "real" disulfides.
Good luck!
Ulla
> Dear all,
>
> I am refining structures containing disulfides using refmac. Many of the
> disulfides are partly broken due to radiation damage.
>
> I tried modeling alternative conformations (i.e. one cysteine pair in a
> disulfide and the other pair as free thiols), but after refinement the
> reduced form is forced back to its original position forming a disulfide
> bridge and resulting in difference density in the fo-fc map.
>
> How do I prevent a disulfide bond from being defined for the free thiol?
>
>
>
> Best regards,
>
> Joel Heim
>
> University of Oslo
>
>
>
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