[phenixbb] Update: Check for radiation-induced reduction of a disulfide bond

Ezequiel Noguera back_noguera at yahoo.com.ar
Mon Feb 15 14:33:58 PST 2016

Thank you for valuable advice of the BB. Negative density is observed between sulfur atoms of the disulfide pair, and positive density at the opposite side of the SG atom. I guess it is partial reduction due to radiation damage. Now, I refined using a altlocs and disulfide_bond_exclusions_selection_string to avoid forming a disulfide by altlocs of SG (because the rotamer is the same that the disulfide pair). Around 70 % occupancy is obtained for reduced Cys, and distances between SG increased near to 3 A. Difference density mostly dissapeared. I suppose is better to model only as disulfide for deposition, because reduction is "artifactual" from biological point of view, but it is other discussion... Thank you!Ezequiel 

    El Lunes, 15 de febrero, 2016 8:41:49, Pavel Afonine <pafonine at lbl.gov> escribió:

  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.

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