[phenixbb] Segmentation fault with twin-law refinement

hari jayaram harijay at gmail.com
Wed Aug 13 11:51:57 PDT 2008


Thanks Paul Adams and Peter Zwart,
The twin-law phenix.refine segmentation-fault problem I had reported
on using phenix 1.3brc6 on my Mac Pro Leopard ver 10.5.4 ,  has
disappeared when I updated to the latest phenix final release 1.3.
Thanks for your help

Hari


On Tue, Aug 12, 2008 at 4:48 PM, Paul Adams <PDAdams at lbl.gov> wrote:
>
> 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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>
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>
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