Re: [phenixbb] unwanted disulfids and geometry restraints

On 6/27/13 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.

yes, I guess you are correct. One can quickly check using: phenix.pdb_interpretation model.pdb write_geo_files=true disulfide_distance_cutoff=0 Pavel