[phenixbb] Segmentation fault with twin-law refinement

Paul Adams PDAdams at lbl.gov
Tue Aug 12 13:48:34 PDT 2008


Please download the latest version of Phenix (1.3 final) to see if  
that fixes the problem.

On Aug 12, 2008, at 1:00 PM, hari jayaram wrote:

> Hi I have discovered that my data in the P3 spacegroup is  
> potentially twinned. Truncate and phenix.xtriage indicate that the  
> twin fraction is pretty high ( between 0.35 and 0.42).
> I am still new to twinned data refinement and still dont know which  
> twin law to pick from the three possibilities for P3 that xtriage  
> lists.
>
> I am emailing because , Regardless of the twin law I try ,  
> phenix.refine crashes with a Segmentation fault on my Mac Pro  
> leopard 10.5.2 running phenix. 1.3b-rc6
> The command that ends with a Python crash and segmentation fault is
>
> Command used:
>
> phenix.refine cy_p10_2_28.1.pdb cy_p10_2_28.1_unique1.mtz  
> simulated_annealing=true model.ncs refinement.main.ncs=true -- 
> overwrite refinement.ncs.excessive_distance_limit=None  
> strategy=group_adp+individual_sites twin_law='-h,-k,l'  
> refinement.input.xray_data.labels=F_p10-2,SIGF_p10-2 >  
> phenix_run2_mhmkl_simulanneal.log
>
>
> phenix.xtriage outputs
>
> Statistics depending on twin laws
> ------------------------------------------------------------------
> | Operator  | type | R obs. | Britton alpha | H alpha | ML alpha |
> ------------------------------------------------------------------
> | -h,-k,l   |   M  | 0.100  | 0.406         | 0.407   | 0.393    |
> | h,-h-k,-l |   M  | 0.071  | 0.426         | 0.439   | 0.458    |
> | -k,-h,-l  |   M  | 0.090  | 0.411         | 0.417   | 0.415    |
> ------------------------------------------------------------------
>
> Can you tell me if there is something I am doing wrong .
> Thanks a tonne for your help
> Hari Jayaram
> Postdoc , Brandeis University
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

-- 
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

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