I agree with Pavel. Disulfides are hit by radiation damage, and I usually observe "partially reduced" disulfides in datasets I collect at synchrotrons. If that is the case, the solution is to create alternate conformations for the cysteines involved. Make sure the reduced cysteines have the same altloc, and are moved into positive mFoFc density, so that Phenix does not automatically link them as disulfides. Engin On 2/15/16 2:46 AM, Pavel Afonine wrote:
P.S.:
If atom is misplaced normally you would see both: positive and negative residual density in close proximity to each other.
If you only see negative density at SG centers this may mean the site is partially occupied.
Pavel
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. Thank you,
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