[bug #17329] Diffusion Tensor PDB creation is broken -- December 16, 2010 - 04:59

URL:
  <http://gna.org/bugs/?17329>

                 Summary: Diffusion Tensor PDB creation is broken
                 Project: relax
            Submitted by: michaelbieri
            Submitted on: Do 16 Dez 2010 14:59:48 EST
                Category: None
                Severity: 3 - Normal
                Priority: 5 - Normal
                  Status: None
                 Privacy: Public
             Assigned to: michaelbieri
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
         Discussion Lock: Any
                 Release: Repository: 1.3 line
        Operating System: None

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Details:

By trying to create a diffusion tensor pdb representation (either after
running the GUI or the diff_tensor_pdb.py script) the following error occurs:

Traceback (most recent call last):
  File "/usr/local/bin/relax", line 390, in <module>
    Relax()
  File "/usr/local/bin/relax", line 123, in __init__
    self.interpreter.run(self.script_file)
  File "/home/michael/Programme/relaxGUI/prompt/interpreter.py", line 290, in
run
    return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
  File "/home/michael/Programme/relaxGUI/prompt/interpreter.py", line 536, in
run_script
    return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
  File "/home/michael/Programme/relaxGUI/prompt/interpreter.py", line 432, in
interact_script
    execfile(script_file, local)
  File "diff_tensor_pdb.py", line 15, in <module>
    structure.create_diff_tensor_pdb(file=tensor_file, force=True)
  File "/home/michael/Programme/relaxGUI/prompt/structure.py", line 148, in
create_diff_tensor_pdb
    generic_fns.structure.geometric.create_diff_tensor_pdb(scale=scale,
file=file, dir=dir, force=force)
  File "/home/michael/Programme/relaxGUI/generic_fns/structure/geometric.py",
line 471, in create_diff_tensor_pdb
    CoM = centre_of_mass()
  File "/home/michael/Programme/relaxGUI/generic_fns/structure/mass.py", line
95, in centre_of_mass
    mass = return_atomic_mass(element)
  File "/home/michael/Programme/relaxGUI/physical_constants.py", line 257, in
return_atomic_mass
    if upper(element) == 'CA':
  File "/usr/lib/python2.6/string.py", line 235, in upper
    return s.upper()
AttributeError: 'NoneType' object has no attribute 'upper'





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