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 <[log in to unmask]> (on behalf
of Pavel Afonine <[log in to unmask]>)
>Subject: Re: [ccp4bb] negative density around disulfide bond
>To: [log in to unmask]
>
> 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
> <[log in to unmask]> 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
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