[phenixbb] Segmentation fault with twin-law refinement

hari jayaram harijay at gmail.com
Tue Aug 12 13:00:50 PDT 2008


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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