Re: [phenixbb] unwanted disulfids and geometry restraints

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. -Nat On Thu, Jun 27, 2013 at 9:17 AM, Ursula Schulze-Gahmen wrote:

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.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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