[bug #7979] Problems with the diffusion tensor PDB representation user function with MC sims. -- December 10, 2006 - 03:20

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

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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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