[phenixbb] anomalous difference map calculation option in phenix.refine

Randy Read rjr27 at cam.ac.uk
Mon Aug 18 02:00:29 PDT 2008

Hi Pavel,

We should compare the anomalous difference maps you get with the  
results of running LLG completion looking for anomalous scatterers in  
Phaser.  In our experiences so far, the LLG maps show the missing  
anomalous scatterers at a higher significance level than the  
corresponding model-phased anomalous difference Fouriers starting from  
the same model.  More importantly, the iterative procedure (where  
anomalous scatterers are added to the model and refined) pulls out  
sites that don't appear in the initial map with either approach.

Once the SAD target is properly implemented in phenix.refine, it  
should be possible to carry out these calculations directly from  
phenix.refine as well.  Ralf and Airlie have promised to get the  
problems sorted out at the next workshop, and I think Ralf is planning  
on coming a few days early.



On 18 Aug 2008, at 01:06, Pavel Afonine wrote:

> For many of you who asked for anomalous difference map calculation
> option in phenix.refine: this is fixed and available in just announced
> PHENIX release.
> Pavel.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
Hills Road                                    E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                       www- 

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