Hi, can you send me data and model? That will make it easy to debug. P 2008/8/12 hari jayaram :

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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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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