URL:
<http://gna.org/bugs/?7979>
Summary: Problems with the diffusion tensor PDB
representation user function with MC sims.
Project: relax
Submitted by: bugman
Submitted on: Sunday 12/10/2006 at 02:20
Category: relax's source code
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: bugman
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: Repository: 1.3 line
Operating System: All systems
_______________________________________________________
Details:
An IndexError occurs when the user function for creating the PDB
representation of the diffusion tensor is used to display the results of
Monte Carlo simulations. The traceback and a few earlier text is:
relax> structure.create_diff_tensor_pdb(run='sims',
scale=1.7999999999999999e-06, file='tensor.pdb', dir=None, force=1)
Chain A
Calculating the centre of mass.
Total mass: M = 16249.115200000038
Centre of mass: R = array([ 0.99814433, -0.25464415, -0.40853369])
Generating the geometric object.
Creating the uniform vector distribution.
Generating the unique axis of the diffusion tensor.
Scaling factor: 1.7999999999999999e-06
Dpar vector (scaled + shifted to R): array([-25.9964777 , 20.81570053,
23.15148718])
Creating the MC simulation axes.
Traceback (most recent call last):
File "/mnt/removable/relax/relax-1.3/relax", line 454, in ?
Relax()
File "/mnt/removable/relax/relax-1.3/relax", line 166, in __init__
self.interpreter.run()
File "/mnt/removable/relax/relax-1.3/prompt/interpreter.py", line 216, in
run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File "/mnt/removable/relax/relax-1.3/prompt/interpreter.py", line 391, in
run_script
console.interact(intro, local, script_file, quit)
File "/mnt/removable/relax/relax-1.3/prompt/interpreter.py", line 343, in
interact_script
execfile(script_file, local)
File "create_tensor.py", line 13, in ?
structure.create_diff_tensor_pdb(name, file='tensor.pdb', force=1)
File "/mnt/removable/relax/relax-1.3/prompt/structure.py", line 169, in
create_diff_tensor_pdb
self.__relax__.generic.structure.create_diff_tensor_pdb(run=run,
scale=scale, file=file, dir=dir, force=force)
File "/mnt/removable/relax/relax-1.3/generic_fns/structure.py", line 408,
in create_diff_tensor_pdb
self.generate_spheroid_axes(chain_id=chain_id, res_num=res_num, R=R,
i=i)
File "/mnt/removable/relax/relax-1.3/generic_fns/structure.py", line 731,
in generate_spheroid_axes
Dpar = self.relax.data.diff[self.run].Dpar_sim[i]
IndexError: list index out of range
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