[phenixbb] unwanted disulfids and geometry restraints
nechols at lbl.gov
Thu Jun 27 09:41:17 PDT 2013
In the short term, just lower the distance cutoff - I suspect 2.0
would be a good starting point as long as the initial model is fairly
accurate. I wouldn't put it all the way at zero (this may have weird
side effects), but any arbitrarily low value will eventually prevent
any disulfides from being formed, if that's what you want.
On Thu, Jun 27, 2013 at 9:17 AM, Ursula Schulze-Gahmen
<uschulze-gahmen at lbl.gov> wrote:
> 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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> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
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