[phenixbb] unwanted disulfids and geometry restraints

Pavel Afonine pafonine at lbl.gov
Thu Jun 27 07:27:31 PDT 2013

On 6/27/13 7:12 AM, Nathaniel Echols wrote:
> On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine <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.

yes, I guess you are correct. One can quickly check using:

phenix.pdb_interpretation model.pdb write_geo_files=true 


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