[phenixbb] unwanted disulfids and geometry restraints

Pavel Afonine pafonine at lbl.gov
Thu Jun 27 09:28:38 PDT 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.


> 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 <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
>     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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