[phenixbb] unwanted disulfids and geometry restraints
drdavidcbriggs at gmail.com
Thu Jun 27 09:32:30 PDT 2013
Fyi, many moons ago when I was building/refining 2iyb, I had to deactivate
automatic disulphide detection to stop my metal sites from doing just this.
This was refmac, so this problem is not confined to phenix.
On Jun 27, 2013 5:29 PM, "Pavel Afonine" <pafonine at lbl.gov> wrote:
> 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.
> 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.
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