Re: [phenixbb] IAS causes phenix.refine to die

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::mpl::vector4 const&, scitbx::af::const_ref const&, bool const&, bool const&>

...

::execute(_object*, scit bx::af::const_ref const&, scitbx::af::cons t_ref 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 const&, scitbx::af::const_ref 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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