[phenixbb] IAS causes phenix.refine to die

[Pavel Afonine]

Hi Anna,

it's a bug, I'm afraid. I remember fixing something related to this a 
couple of months ago. Could you please try the latest available version 
of PHENIX:
http://www.phenix-online.org/download/

Pavel.


On 1/23/2009 4:25 PM, Anna Gardberg wrote:
> Dear phenix list,
>
> My 0.75 A refinement has some problems in its higher resolution bins, 
> so I thought I might try adding in IAS scatterers. However, the 
> phenix.refine (version 2008_09_13_0905) crashed when I set "ias = 
> True". I hope someone here can help me figure out the problem. I 
> include snippets of output below, as the entire error message was very 
> lengthy. Am I misusing the command, is there a problem with my system 
> setup, or what?
>
> Regards,
> Anna Gardberg
>
>                      ----------Building IAS 
> model----------                   
>
> >>> Adding IAS..........
> Total number of covalent bonds =  895
> show_stack(1): 
> /home/a1g/downloads/cci_apps_sources/mmtbx/ias/__init__.py(438) _
> _init__
> show_stack(2): 
> /home/a1g/downloads/cci_apps_sources/mmtbx/ias/__init__.py(371) s
> et_peaks
> show_stack(3): 
> /home/a1g/downloads/cci_apps_sources/mmtbx/ias/__init__.py(616) _
> _init__
> show_stack(4): 
> /home/a1g/downloads/cci_apps_sources/mmtbx/model.py(494) add_ias
> show_stack(5): 
> /home/a1g/downloads/cci_apps_sources/phenix/phenix/refinement/str
> ategies.py(409) refinement_machine
> show_stack(6): 
> /home/a1g/downloads/cci_apps_sources/phenix/phenix/refinement/dri
> ver.py(1082) run
>
> <snip pages of output>
>
>   
> /home/a1g/downloads/cci_apps_build/lib/cctbx_maptbx_ext.so(boost::python::obje
> cts::make_holder<4>::apply<boost::python::objects::value_holder<cctbx::maptbx::o
> ne_gaussian_peak_approximation>, 
> boost::mpl::vector4<scitbx::af::const_ref<doubl
> e, scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double, 
> scitbx::a
> f::trivial_accessor> const&, bool const&, bool const&> 
> >::execute(_object*, scit
> bx::af::const_ref<double, scitbx::af::trivial_accessor> const&, 
> scitbx::af::cons
> t_ref<double, scitbx::af::trivial_accessor> const&, bool const&, bool 
> const&)+0x
> 75c) [0x2a9d79598c]
>   
> /home/a1g/downloads/cci_apps_build/lib/cctbx_maptbx_ext.so(cctbx::maptbx::find
> _gaussian_parameters::find_gaussian_parameters(scitbx::af::const_ref<double, 
> sci
> tbx::af::trivial_accessor> const&, scitbx::af::const_ref<double, 
> scitbx::af::tri
> vial_accessor> const&, double const&, double const&, double)+0x3fe) 
> [0x2a9d7827f
> e]
>   /lib64/tls/libm.so.6 [0x32ee506263]
>   /lib64/tls/libc.so.6 [0x32ee22e300]
> Floating-point error (Python and libc call stacks above)
> [1]+  Done                    gedit newscale-ias.eff
>
> ------------------------------------------------------------------------
>
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>   
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