Hi Ed,
Everything seems cool ! I get to know the code much more, but may make
some errors and introduce new bugs...
Additionally, I a currently stuck with the message error for
diffusion_tensor system test :
========
line :
Traceback (most recent call last):
File
"/home/semor/pse-4/collaborations/relax/relax-1.3/test_suite/system_tests/diffusion_tensor.py",
line 109, in test_createDiffTensor
self.relax.interpreter._Structure.create_diff_tensor_pdb(file='devnull')
File
"/home/semor/pse-4/collaborations/relax/relax-1.3/prompt/structure.py",
line 167, in create_diff_tensor_pdb
generic_fns.structure.geometric.create_diff_tensor_pdb(scale=scale,
file=file, dir=dir, force=force)
File
"/home/semor/pse-4/collaborations/relax/relax-1.3/generic_fns/structure/geometric.py",
line 263, in create_diff_tensor_pdb
res_num = generate_vector_residues(structure=structure,
vector=pipe.diff_tensor.Dpar*pipe.diff_tensor.Dpar_unit,
atom_name='Dpar', res_name_vect='AXS', sim_vectors=sim_vectors,
chain_id=chain_id, res_num=res_num, origin=R, scale=scale, neg=True)
NameError: global name 'R' is not defined
========
I tried (pessimistly) setting R to different things :
- pipe.diff_tensor.rotation
- centre_of_mass()
- eye(3)
- None
but none would work (!) and I am now without idea... Do you have any
clue ? Did I break something somewhere else yesterday ?
Moreover, the system test doesn't stop at the first instance of
structure.create_diff_tensor_pdb(), but at the second, the first being
the one for the sphere. Hence, the sphere representation doesn't fail,
but I tried it with a script of my own and it yields an empty pdb
(except for the header). Would you have a tensor pdb I could look at so
when the code works again, I know the file is correctly formatted..?
Regards,
Séb
Edward d'Auvergne wrote:
> Hi,
>
> With the fixes you've been making and the changes I made to the
> structural object code, I think the diffusion tensor representation
> should soon be functioning again. Do you see any real technical
> issues preventing this? I hope my changes haven't caused you too many
> problems. They were necessary though, as the PDB reading and writing
> code was broken.
>
> Regards,
>
> Edward
>
>
> On Tue, Jul 8, 2008 at 6:42 AM, <[EMAIL PROTECTED]> wrote:
>
>> Author: semor
>> Date: Tue Jul 8 06:42:46 2008
>> New Revision: 6834
>>
>> URL: http://svn.gna.org/viewcvs/relax?rev=6834&view=rev
>> Log:
>> Corrected a typo introduced in r6815.
>>
>>
>> Modified:
>> 1.3/generic_fns/structure/geometric.py
>>
>> Modified: 1.3/generic_fns/structure/geometric.py
>> URL:
>> http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=6834&r1=6833&r2=6834&view=diff
>> ==============================================================================
>> --- 1.3/generic_fns/structure/geometric.py (original)
>> +++ 1.3/generic_fns/structure/geometric.py Tue Jul 8 06:42:46 2008
>> @@ -611,7 +611,7 @@
>> atom_id_ext = ''
>>
>> # The origin atom.
>> - structure.atom_add(pdb_record='HETATM', atom_num='R_vect'+atom_id_ext,
>> atom_name=R, res_name=res_name_vect, chain_id=chain_id, res_num=res_num,
>> pos=origin, segment_id=None, element='C', struct_index=None)
>> + structure.atom_add(pdb_record='HETATM', atom_num='R_vect'+atom_id_ext,
>> atom_name='R', res_name=res_name_vect, chain_id=chain_id, res_num=res_num,
>> pos=origin, segment_id=None, element='C', struct_index=None)
>>
>> # Create the PDB residue representing the vector.
>> structure.atom_add(pdb_record='HETATM', atom_num=atom_name+atom_id_ext,
>> atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id,
>> res_num=res_num, pos=origin+vector*scale, segment_id=None, element='C',
>> struct_index=None)
>>
>>
>> _______________________________________________
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>>
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>
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