[phenixbb] Segmentation fault with twin-law refinement

hari jayaram harijay at gmail.com
Tue Aug 12 13:16:55 PDT 2008


Thanks a lot peter
Here they are
http://mango.biochem.brandeis.edu/~hari/cy_p10_2_28.1_unique1.mtz

And
http://mango.biochem.brandeis.edu/~hari/cy_p10_2_28.1.pdb

Let please do not hesitate to let me know if you need anything else.

Hari

On Tue, Aug 12, 2008 at 4:09 PM, Peter Zwart <PHZwart at lbl.gov> wrote:

> Hi,
>
> can you send me data and model? That will make it easy to debug.
>
> P
>
> 2008/8/12 hari jayaram <harijay at gmail.com>:
> > 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
> >
> >
>
>
>
> --
> -----------------------------------------------------------------
> P.H. Zwart
> Beamline Scientist
> Berkeley Center for Structural Biology
> Lawrence Berkeley National Laboratories
> 1 Cyclotron Road, Berkeley, CA-94703, USA
> Cell: 510 289 9246
> BCSB: http://bcsb.als.lbl.gov
> PHENIX: http://www.phenix-online.org
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