Re: [phenixbb] unwanted disulfids and geometry restraints

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 wrote:

On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine 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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