Hi Ed, The test passes when doing this change (since R is now defined).
When using my script, I get a tensor pdb, but it is empty... since this is the same change as setting : R = centre_of_mass()... Any clue ? If the change of R to CoM is ok (within the create_diff_tensor_pdb() function), then maybe other changes are needed elsewhere... I'll commit these changes anyway. We can still revert later on if this is wrong. Regards, Séb Edward d'Auvergne wrote: > Sorry, I couldn't check the sources to find this as my computer is > having hardware failures at the moment. But what you have found is > very likely to be the problem, and just changing all references to the > R variable to CoM should fix it. > > Cheers, > > Edward > > > On Tue, Jul 8, 2008 at 6:27 PM, Sébastien Morin > <[EMAIL PROTECTED]> wrote: > >> Hi Ed, >> >> I looked at the code using svn diff with revision number... >> >> It seems that line 225 of generic_fns/structure/geometric.py was changed >> from : >> >> R = centre_of_mass() >> >> to >> >> CoM = centre_of_mass() >> >> So, should we change the following calls to 'R' to calls to 'CoM' ? Or >> am I completely wrong..? >> >> Cheers, >> >> >> Séb >> >> >> >> >> Edward d'Auvergne wrote: >> >>> Hi, >>> >>> Yeah, I noticed that problem in your test. I'll try to hunt down a >>> little later where we lost this R array (the origin set to the centre >>> of mass). It should be documented in the changes in this method >>> (using svn diff with revision numbers will be useful) that have >>> occurred in the 1.3 line. >>> >>> Regards, >>> >>> Edward >>> >>> >>> On Tue, Jul 8, 2008 at 3:32 PM, Sébastien Morin >>> <[EMAIL PROTECTED]> wrote: >>> >>> >>>> 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) >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> relax (http://nmr-relax.com) >>>>>> >>>>>> This is the relax-commits mailing list >>>>>> [EMAIL PROTECTED] >>>>>> >>>>>> 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 >>>>> [email protected] >>>>> >>>>> 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 >>>>> >>>>> >>>>> >>>>> >>> >> > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] 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
