Hi Ursula,

could you please send me the model and data files off list and indicate unwanted S-S bonds? I may just implement automatic (or at least easier than now) handling of this today or over the week-end.

Thanks,
Pavel

So how do people deal with this? I would think close cysteines are fairly common in metal coordination sites.

Ursula

On Thu, Jun 27, 2013 at 7:12 AM, Nathaniel Echols <[email protected]> wrote:
On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine <[email protected]> wrote:
> Hm.. this isn't easy.. phenix.refine automatically identifies disulfide
> bonds and creates restrains for them. This is controlled by
> disulfide_distance_cutoff=3 parameter. You can set it to some big number, so
> none desulfide bonds will be created automatically

Are you sure it's not the reverse?  I think this number sets the
maximum distance allowed for disulfides; increasing it will just bond
more distant atoms.

-Nat