[phenixbb] unwanted disulfids and geometry restraints

Ursula Schulze-Gahmen uschulze-gahmen at lbl.gov
Thu Jun 27 09:17:22 PDT 2013

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


On Thu, Jun 27, 2013 at 7:12 AM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine <pafonine at lbl.gov> 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
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Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220
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