Re: diffusion tensor -- March 13, 2013 - 17:31

Sorry once again. In fact relax has chosen the 'local_tm" however I don't get 
any diffusion tensor even selecting on the user function menu the 
diffusion_tensor.display says:

"RelaxError: No diffusion tensor data exists"

I think this might be normal for the local_tm model once it assumes the 
molecule doesn't  diffuse as a globular protein and somehow none of the 
models fits the data?!
However, this result is quite strange since my protein is quite spherical and 
the inertia tensors are 1: 0.8: 0.7

Any ideas?

many thanks,
Angelo

On 13 Mar 2013, at 13:07, Edward d'Auvergne wrote:

> Hi Angelo,
>
> Welcome to the relax mailing lists!  The problem you are seeing is a
> clear bug.  Would you be able to submit a bug report using the link
> https://gna.org/bugs/?func=additem&group=relax ?  Thanks.  Although
> bug #12408 (https://gna.org/bugs/?12408) appears to be similar, this
> is only because both cases use the special RelaxNoTensorError error
> object.  For the bug report, would you be able to include the output
> of:
>
> $ relax --info
>
> Also if you could look at the logs and say which global diffusion
> model was selected, that would be useful.  And have you used a 3D
> structure file for the analysis?
>
> Note that this failure has occurred at the very end of the analysis.
> The call to the structure.create_diff_tensor_pdb user function is the
> very last thing that this model-free auto-analysis does (you can see
> that here if you are interested,
> http://www.nmr-relax.com/api/auto_analyses.dauvergne_protocol-pysrc.html#dAuvergne_protocol.execute).
> Therefore this error is not too important for your analysis.  It
> would be good to have the bug report though so that I can come up with
> a solution.
>
> Cheers,
>
> Edward
>
>
>
> On 13 March 2013 13:43, Angelo Miguel Figueiredo
> <am.figueiredo@xxxxxxxxxx> wrote:
> > Dear relax community,
> >
> > I am a new user that recently installed relax 2.2.2. After been playing
> > around with it I spot in the late stage of my final calculation the
> > following message in attach.
> >
> > Does anybody has a clue or advice what could be wrong with it. I spot a
> > similar error in earlier relax versions (bug #12408) but I am not sure if 
> > it
> > is the same issue, apparently relax can't read/load my diffusion tensor.
> >
> > Any help will be appreciated.
> >
> > Many thanks,
> > Angelo
> >
> >
> >
> > relax> structure.create_diff_tensor_pdb(scale=1.8e-06, file='tensor.pdb',
> > dir='/home/final', force=True)
> > Exception raised in thread.
> >
> > Traceback (most recent call last):
> > File "/home/angelo/Software/relax-2.2.2/gui/analyses/execute.py", line 87,
> > in run
> > self.run_analysis()
> > File "/home/angelo/Software/relax-2.2.2/gui/analyses/auto_model_free.py",
> > line 808, in run_analysis
> > dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name,
> > pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir,
> > diff_model=self.data.global_models, mf_models=self.data.mf_models,
> > local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc,
> > diff_tensor_grid_inc=self.data.diff_tensor_grid_inc,
> > mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter,
> > conv_loop=self.data.conv_loop)
> > File
> > "/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py",
> > line 234, in __init__
> > self.execute()
> > File
> > "/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py",
> > line 745, in execute
> > self.write_results()
> > File
> > "/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py",
> > line 937, in write_results
> > self.interpreter.structure.create_diff_tensor_pdb(file="tensor.pdb",
> > dir=dir, force=True)
> > File "/home/angelo/Software/relax-2.2.2/prompt/uf_objects.py", line 219, in
> > __call__
> > self._backend(*new_args, **uf_kargs)
> > File 
> > "/home/angelo/Software/relax-2.2.2/generic_fns/structure/geometric.py",
> > line 449, in create_diff_tensor_pdb
> > raise RelaxNoTensorError('diffusion')
> > RelaxNoTensorError: RelaxError: No diffusion tensor data exists.
> >
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