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 <[email protected]> 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 > <[email protected]> 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/ >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel >> > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
