[phenixbb] unwanted disulfids and geometry restraints

[David Briggs]

Hi all,

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.

Dave
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.
>
> 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 <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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>
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