[bug #21561] generate_vector_residues fails because sim_axes is empty -- January 30, 2014 - 16:43

URL:
  <http://gna.org/bugs/?21561>

                 Summary: generate_vector_residues fails because sim_axes is
empty
                 Project: relax
            Submitted by: mab
            Submitted on: Thu 30 Jan 2014 03:43:04 PM GMT
                Category: relax's source code
                Severity: 3 - Normal
                Priority: 5 - Normal
                  Status: None
                 Privacy: Public
             Assigned to: None
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
         Discussion Lock: Any
                 Release: Repository: trunk
        Operating System: All systems

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Details:

Hi Edward,

when I attempted to write out a PDB with the diffusion tensor representation
with structure.create_diff_tensor_pdb() I encountered the error given below
while the axes are being generated. The reason is that the sim_axes array is
empty. After commenting out the "res_num = generate_vector_residues(..)" line
in the "diffusion tensor" function, the PDB file is successfully written out,
but without the axes of course. 

I could reproduce this with two different results files, that's why I guess
the error is not on my side ...

structure.create_diff_tensor_pdb(file='tensor.pdb')
RelaxWarning: Skipping the atom '#XYZ_mol1:276@4348' as the element type
cannot be determined.
Calculating the centre of mass.
    Total mass:      M = 29614.32293999924
    Centre of mass:  R = array([ 11.448397084650981,  -4.185113042165101,  
6.027848657532893])

Generating the geometric object.
    Creating the uniform vector distribution.

Generating the unique axis of the diffusion tensor.
    Scaling factor:                      1.8e-06
Traceback (most recent call last):
  File "<console>", line 1, in <module>
  File "/usr/local/Cellar/relax/3.1.1/prompt/uf_objects.py", line 221, in
__call__
    self._backend(*new_args, **uf_kargs)
  File "/usr/local/Cellar/relax/3.1.1/pipe_control/structure/main.py", line
272, in create_diff_tensor_pdb
    diffusion_tensor(mol=mol, tensor=pipe.diff_tensor.tensor,
tensor_diag=pipe.diff_tensor.tensor_diag, diff_type=diff_type,
rotation=pipe.diff_tensor.rotation, axes=axes, sim_axes=sim_axes, com=com,
scale=scale)
  File
"/usr/local/Cellar/relax/3.1.1/lib/structure/represent/diffusion_tensor.py",
line 100, in diffusion_tensor
    res_num = generate_vector_residues(mol=mol, vector=axes[0],
atom_name='Dpar', res_name_vect='AXS', sim_vectors=sim_axes[0],
res_num=res_num, origin=com, scale=scale, neg=True)
IndexError: list index out of range






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