[phenixbb] IAS causes phenix.refine to die

[Anna Gardberg]

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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