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
