[phenixbb] IAS causes phenix.refine to die
Pavel Afonine
pafonine at lbl.gov
Sat Jan 24 11:44:18 PST 2009
Hi Anna,
I just thought the following might be helpful for your refinement at
ultra-high resolution:
- you may need to do the refinement with very relaxed or even turned off
geometry and ADP restraints. Even if a few disordered parts of your
structure get distorted after that, you can regularize them later;
- keep "ordered_solvent" option set True. You may need to relax water
picking criteria;
- check for alternative conformations: at this resolution you may
observe plenty of them;
- if residual map shows bonding density, add IAS;
- you may see one or two peaks residual density peaks around water
oxygens: these are hydrogens. phenix.refine has an option to
automatically add H atoms to water based on mFo-DFc map;
- check to see if you have and modeled crystallization solution
components, like ions and other small molecules;
- at this resolution, ADP of water oxygens should be refined as anisotropic;
- of course, hydrogens should be added;
- at this resolution, the R-factor is usually less than 10% and Rfree
usually higher by ~1-2%. Yes, the R-factor if often pretty high in high
resolution bins.
Cheers,
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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