[phenixbb] phenix.real_space_refine

Pavel Afonine pafonine at lbl.gov
Thu May 15 21:36:17 PDT 2014


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:   gino.cingolani at jefferson.edu
> Website:  http://www.cingolanilab.org
> ******************************************************************************
> "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"
> ("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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