[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.

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 
> <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
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130627/9a68cc83/attachment.htm>


More information about the phenixbb mailing list