[phenixbb] disulfide bonds in phenix.refine

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Fri Jan 18 12:07:31 PST 2008

Hi Allister,

> 1) How do I specifically prevent a disulfide bond from being defined
> between two sulfurs that are close together (I tried manipulating the
> "disulfide_distance_cutoff" variable but this doesn't seem to stop a
> disulfide being formed).

If you set, e.g.


you shouldn't get any disulfide bonds anymore. I just tried it on a
small structure and it worked as expected.

> 2)  How can I soften the restraint on the disulfide bond length for
> specific cysteine residues.

With the current phenix.refine you cannot edit the automatically
determined disulfide bonds (sorry). However, you can use
disulfide_distance_cutoff=0.1 to turn off the automatic
bonds. Then use geometry_restraints.edits (see documentation at
http://phenix-online.org/documentation/refinement.htm) to define the
disulfides manually one by one, with the ideal distances and sigmas
you want to use. Use a log file from a previous phenix.refine run
to obtain the list of all disulfides.


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