What does an omit map look like, if you omit both cysteines? Best wishes, Reza
Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org ---- Original message ---- >Date: Mon, 2 Jun 2014 09:31:28 -0700 >From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> (on behalf of Pavel Afonine <pafon...@gmail.com>) >Subject: Re: [ccp4bb] negative density around disulfide bond >To: CCP4BB@JISCMAIL.AC.UK > > Ezequiel, > since you mentioned you tried Phenix too: > in Phenix you can remove a particular disulfide bond > by using a parameter, for**example: > > disulfide_bond_exclusions_selection_string="(chain A > and resseq 1 and name SG) or (chain B and resseq 10 > and name SG)" > > This works in the command line and GUI. Please let > me know (off-list) if you any help with this. > > Pavel > > On Sun, Jun 1, 2014 at 10:08 PM, Eze Chivi > <ezech...@outlook.com.ar> wrote: > > Hello, when I refine my structure, I see negative > density around the disulfide bond. I have 7 copies > per ASU, and I can see this density in many of > them. In some cases, I see positive density also > (negative in the center of the straight line > linking S atoms, and positive in both sides). What > can I try to solve it? Is it due to radiation > damage? Alternative conformation (partial > oxidation)? Incorrect disulfide geometry > parameters? My resolution is 2.1 A, R/Rfree are > around 0.220/0.243, and similar results with > refmac5, phenix and PDBREDO. Please find two > example pictures in attachment. > Thanks for your help! > > Ezequiel
