[phenixbb] unwanted disulfids and geometry restraints
pafonine at lbl.gov
Thu Jun 27 09:28:38 PDT 2013
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.
> 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
> <mailto:nechols at lbl.gov>> wrote:
> On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine <pafonine at lbl.gov
> <mailto:pafonine at lbl.gov>> wrote:
> > Hm.. this isn't easy.. phenix.refine automatically identifies
> > 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.
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