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, <sebastien.morin.1@xxxxxxxxx> 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)
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-commits mailing list
relax-commits@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-devel mailing list
relax-devel@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-devel
Re: r6834 - /1.3/generic_fns/structure/geometric.py