Hi Gino,

phenix.real_space_refine is actively developing tool; a week old version is an obsolete one. So please try the latest one from nightly builds:

http://phenix-online.org/download/nightly_builds.cgi

and if this does not work please send me input files so I investigate.

Specifically in this case the program crashed because the origin of input map is not zero. In recent versions this is fixed.

Pavel

On 5/15/14, 2:58 PM, Gino Cingolani wrote:

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




******************************************************************************
Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
Office (215) 503 4573
Lab    (215) 503 4595
Fax    (215) 923 2117
E-mail:   [email protected]
Website:  http://www.cingolanilab.org
******************************************************************************
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("You were not born to live like brutes, but to follow virtue and knowledge")
Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120)

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