bugrelax - Bugs: bug #21561, generate_vector_residues fails...

 
 
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bug #21561: generate_vector_residues fails because sim_axes is empty (failure of the structure.create_diff_tensor_pdb user function)

Submitted by:  Martin Ballaschk <mab>
Submitted on:  Thu 30 Jan 2014 03:43:04 PM UTC  
 
Category: relax's source codeSpecific analysis category: Model-free analysis
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: Repository: trunkOperating System: All systems

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Thu 30 Jan 2014 05:10:15 PM UTC, SVN revision 22079:

Merged revisions 22078 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22078 | bugman | 2014-01-30 18:02:35 +0100 (Thu, 30 Jan 2014) | 9 lines

Fix for bug #21561, the structure.create_diff_tensor_pdb user function failure with no simulations.

Bug #21561 (https://gna.org/bugs/?21561) was reported by Martin Ballaschk
(https://gna.org/users/mab).

The problem was that the simulation axes of the tensor PDB file were not being initialised correctly
when no Monte Carlo simulations had been run.
........

(Browse SVN revision 22079)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 30 Jan 2014 05:02:35 PM UTC, SVN revision 22078:

Fix for bug #21561, the structure.create_diff_tensor_pdb user function failure with no simulations.

Bug #21561 (https://gna.org/bugs/?21561) was reported by Martin Ballaschk
(https://gna.org/users/mab).

The problem was that the simulation axes of the tensor PDB file were not being initialised correctly
when no Monte Carlo simulations had been run.

(Browse SVN revision 22078)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 30 Jan 2014 04:59:16 PM UTC, SVN revision 22077:

Merged revisions 22075 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22075 | bugman | 2014-01-30 17:32:34 +0100 (Thu, 30 Jan 2014) | 9 lines

Created the Diffusion_tensor.test_bug_21561_tensor_pdb_failure system test.

This is to catch bug #21561 (https://gna.org/bugs/?21561), as reported by Martin Ballaschk
(https://gna.org/users/mab).

This catches the failure of the structure.create_diff_tensor_pdb user function for non-spherical
diffusion tensors when no Monte Carlo simulations are present.
........

(Browse SVN revision 22077)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 30 Jan 2014 04:32:34 PM UTC, SVN revision 22075:

Created the Diffusion_tensor.test_bug_21561_tensor_pdb_failure system test.

This is to catch bug #21561 (https://gna.org/bugs/?21561), as reported by Martin Ballaschk
(https://gna.org/users/mab).

This catches the failure of the structure.create_diff_tensor_pdb user function for non-spherical
diffusion tensors when no Monte Carlo simulations are present.

(Browse SVN revision 22075)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 30 Jan 2014 03:43:04 PM UTC, original submission:

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

Martin Ballaschk <mab>

 

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  • -unavailable- added by bugman (Updated the item)
  • -unavailable- added by mab (Submitted the item)
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    Follow 6 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 04 Feb 2014 02:58:42 PM UTCbugmanSpecific analysis categoryNone=>Model-free analysis
    Thu 30 Jan 2014 05:02:43 PM UTCbugmanStatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
    Thu 30 Jan 2014 04:45:01 PM UTCbugmanSummarygenerate_vector_residues fails because sim_axes is empty=>generate_vector_residues fails because sim_axes is empty (failure of the structure.create_diff_tensor_pdb user function)
    Thu 30 Jan 2014 04:22:44 PM UTCbugmanAssigned toNone=>bugman
    Thu 30 Jan 2014 04:22:43 PM UTCbugmanStatusNone=>Confirmed
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