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
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@lbl.gov> wrote:
On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine <pafonine@lbl.gov> wrote:Are you sure it's not the reverse? �I think this number sets the
> 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
maximum distance allowed for disulfides; increasing it will just bond
more distant atoms.
-Nat
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