[phenixbb] Anomalous signal

[Randy Read]

In either Phenix or CCP4 you can use Phaser in MR-SAD mode, giving the final refined structure as a partial “MR” model.  If you look for atom type AX (a purely imaginary scatterer with f+f’=0, f”=1), the refined occupancy of a site that is found in this process can be interpreted as the product of the occupancy of the real atom and the f” of that atom.

Alternatively, within Phenix, this is part of a tool integrated into phenix.refine, which also uses other information (such as geometry) to try to identify elemental ions in your structure.  This is done with the “Place elemental ions” option under the “Refinement settings” tab.

Best wishes,

Randy Read

-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research     Tel: +44 1223 336500
The Keith Peters Building                               Fax: +44 1223 336827
Hills Road                                                       E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                              www-structmed.cimr.cam.ac.uk

> On 5 Nov 2020, at 09:32, Gergő Gógl <gogl.gergo at gmail.com> wrote:
> 
> You can try with ANODE to get an anomalous map for your structure. 
> 
> Gergo
> 
> Roger Rowlett <rrowlett at colgate.edu> ezt írta (időpont: 2020. nov. 5., Cs, 1:06):
> You may not need to see an anomalous signal to determine if zinc is bound unless you are trying to discriminate from other metals. Zinc will have characteristic coordination geometry (tetrahedral typically) and characteristic Zn-N and Zn-O bond lengths close to 2.0 A.
> 
> Roger Rowlett
> 
> On Wed, Nov 4, 2020, 4:59 PM Shramana Chatterjee <schatter90 at gmail.com> wrote:
> Hi,
> 
> How can I find anomalous signal for Zn-metal to be sure whether Zn is binding or not, for an already processed dataset? 
> 
> It would be very helpful if I get any suggestion.
> 
> Thank you in advance.
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