Re: [bug #17329] Diffusion Tensor PDB creation is broken -- September 22, 2011 - 11:12

Hi Michael,

Would you know if this bug still exists?  I cannot reproduce this as
this is dependent upon the input PDB file.  Somehow the internal PDB
reader cannot determine the element type of certain atoms, and I have
a feeling this is not yet fixed.

Cheers,

Edward


On 11 January 2011 10:00, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Hi,
>
> Would you have a PDB file and a mini-script with truncated data (or
> set of instructions for the GUI) to be able to reproduce this bug?
> This looks like the internal PDB reader has been used on a PDB file
> with the element column missing, and that the internal reader cannot
> determine the element type of one of the important atoms.
>
> Cheers,
>
> Edward
>
>
>
> On 16 December 2010 04:59, Michael Bieri
> <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> > 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
> >
> >    _______________________________________________________
> >
> > 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'
> >
> >
> >
> >
> >
> >    _______________________________________________________
> >
> > Reply to this item at:
> >
> >  <http://gna.org/bugs/?17329>
> >
> > _______________________________________________
> >  Nachricht geschickt von/durch Gna!
> >  http://gna.org/
> >
> >
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