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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