Hi Ezequiel,

Sorry, my previous email was incomplete. My structure has negative density in the center of some disulfides (the magnitude of this effect vary between different monomers in the ASU). I'd like to refine the structure in an "artificial reduced form", where cysteines involved in disulfides are treated in reduced form, but repulsions originating from neighboring sulfur atoms are turned-off, to monitor distances (I expect that SG atoms remain close to 2 A), guided only by data.

there is no option like "disable non-bonded repulsions in a sphere R=??? Angstroms around given atom". However, there are couple of tricks to do what you want, such as defining bonds between atoms in question with large sigma which will make them invisible to restraints and also disable repulsions. Or playing with altlocs.

You can check .geo file to see exactly what restraints atom in question participates in.

Pavel