[cctbxbb] phenix.map_value_at_point does not work with ccp4 maps

Takanori Nakane takanori.nakane at bs.s.u-tokyo.ac.jp
Fri Dec 11 01:09:40 PST 2015


Dear all,

I encountered an error with phenix.map_value_at_point.
It does not work when ccp4 maps are provided. It works fine
when an mtz file with map coefficients is provided.

Probably this is related to the bug reported last September.
http://phenix-online.org/pipermail/cctbxbb/2015-September/001155.html

It also has a problem that when there are multiple columns in an mtz
file and the specified label does not match any of them, the
last column is used without warning.

phenix.fetch_pdb 3eml
phenix.fetch_pdb -x 3eml
phenix.maps 3eml.pdb 3eml-sf.cif

# Just to use the latest svn version
cctbx.python 
~/prog/dials/modules/cctbx_project/mmtbx/command_line/map_value_at_point.py 
point="1.0 2.0 3.0" 3eml_2mFo-DFc_map.ccp4

Default params::

   label = None
   point = None
   resolution_factor = 0.25
   scale = *sigma volume
   resolution = None
   low_resolution = None

Map values at specified points:
Traceback (most recent call last):
   File 
"/mnt/wd_storage/nakane/prog/dials/modules/cctbx_project/mmtbx/command_line/map_value_at_point.py", 
line 162, in <module>
     run(sys.argv[1:])
   File 
"/mnt/wd_storage/nakane/prog/dials/modules/cctbx_project/mmtbx/command_line/map_value_at_point.py", 
line 146, in run
     "%10.3f"%map_3d.eight_point_interpolation(point_frac)).strip()
Boost.Python.ArgumentError: Python argument types in
     cctbx_maptbx_ext.eight_point_interpolation(double, tuple)
did not match C++ signature:
     eight_point_interpolation(scitbx::af::const_ref<double, 
scitbx::af::c_grid_padded<3ul, unsigned long> >, scitbx::vec3<double>)

cctbx.python 
~/prog/dials/modules/cctbx_project/mmtbx/command_line/map_value_at_point.py 
3eml_map_coeffs.mtz point="1.0 2.0 3.0" label="2FOFCWT" # This works fine

cctbx.python 
~/prog/dials/modules/cctbx_project/mmtbx/command_line/map_value_at_point.py 
3eml_map_coeffs.mtz point="1.0 2.0 3.0" label="WRONG_LABEL" # but this 
also proceeds!

Best regards,

Takanori Nakane


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