[phenixbb] Segmentation fault with twin-law refinement

Pavel Afonine PAfonine at lbl.gov
Tue Aug 12 13:38:39 PDT 2008


Hi,

just a remark. Your data is 2.2A resolution with the R-factors around 
30% and the command below tells me that you are refining group B-factors 
with one isotropic B per residue. This is most likely not what you 
really want to do at this resolution. I would definitely switch to 
individual ADP refinement (strategy=individual_adp+individual_sites).

Pavel.


On 8/12/2008 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
> ------------------------------------------------------------------------
>
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