Re: [phenixbb] unwanted disulfids and geometry restraints

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" 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 wrote:

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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.

-Nat

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