Hi all,
I'm trying to refine a pdb against an EM map using phenix.real_space_refine using default parameters (e.g. phenix.real_space_refine model1.pdb map.ccp4).
The program starts OK but quickly stops with the following output (see below)
Any thoughts? Thanks so much!
Gino
###########################################################################
Add C-beta restraints
*********************
Adding C-beta torsion restraints...
num c-beta restraints: 11832
-------------------------------------------------------------------------------
Getting target map
******************
Traceback (most recent call last):
File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 494, in <module>
o = run(sys.argv[1:])
File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 273, in __init__
self.caller(func = self.get_target_map, prefix="Getting target map")
File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 298, in caller
func(prefix=prefix)
File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 372, in get_target_map
number_of_macro_cycles = self.params.refinement.macro_cycles)
File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 153, in extract_target_map_data_and_crystal_gridding
crystal_symmetry = inputs.xray_structure.crystal_symmetry())
File "/usr/local/phenix-dev-1615/cctbx_project/mmtbx/utils/__init__.py", line 3094, in structure_factors_from_map
use_sg = True)
File "/usr/local/phenix-dev-1615/cctbx_project/cctbx/miller/__init__.py", line 1309, in structure_factors_from_map
assert map.focus_size_1d() > 0 and map.nd() == 3 and map.is_0_based()
AssertionError
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