Re: [phenixbb] unwanted disulfids and geometry restraints

27 Jun 2013

      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 mailto:[email protected]> wrote:
On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine mailto:[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