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<p>Hi all,</p>
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</p>
<p>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).
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<p>The program starts OK but quickly stops with the following output (see below)</p>
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<p>Any thoughts? Thanks so much!</p>
<p><br>
</p>
<p>Gino<br>
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<p><br>
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<p>###########################################################################</p>
<p>Add C-beta restraints<br>
*********************<br>
Adding C-beta torsion restraints...<br>
num c-beta restraints: 11832<br>
-------------------------------------------------------------------------------<br>
Getting target map<br>
******************<br>
Traceback (most recent call last):<br>
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><br>
o = run(sys.argv[1:])<br>
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__<br>
self.caller(func = self.get_target_map, prefix="Getting target map")<br>
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<br>
func(prefix=prefix)<br>
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<br>
number_of_macro_cycles = self.params.refinement.macro_cycles)<br>
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<br>
crystal_symmetry = inputs.xray_structure.crystal_symmetry())<br>
File "/usr/local/phenix-dev-1615/cctbx_project/mmtbx/utils/__init__.py", line 3094, in structure_factors_from_map<br>
use_sg = True)<br>
File "/usr/local/phenix-dev-1615/cctbx_project/cctbx/miller/__init__.py", line 1309, in structure_factors_from_map<br>
assert map.focus_size_1d() > 0 and map.nd() == 3 and map.is_0_based()<br>
AssertionError<br>
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<div style="font-family:Tahoma; font-size:13px"><font style="font-family:Helvetica" size="3">******************************************************************************<br>
Gino Cingolani, Ph.D.<br>
Associate Professor<br>
Thomas Jefferson University<br>
Dept. of Biochemistry & Molecular Biology<br>
233 South 10th Street - Room 826<br>
Philadelphia PA 19107<br>
Office (215) 503 4573<br>
Lab (215) 503 4595<br>
Fax (215) 923 2117<br>
E-mail: gino.cingolani@jefferson.edu<br>
Website: http://www.cingolanilab.org<br>
******************************************************************************<br>
"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"<br>
("You were not born to live like brutes, but to follow virtue and knowledge") <br>
Dante, The Divine Comedy<i><b> </b></i>(<i>Inferno</i>, XXVI, vv. 119-120)<br>
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