Hi Angelo, I'm not sure if you have seen this as you may not be subscribed to the relax-announce mailing list (https://mail.gna.org/listinfo/relax-announce), but a new version of relax has been released fixing the bugs you have encountered. The following link describes the different ways in which you can find out about new relax releases:
http://article.gmane.org/gmane.science.nmr.relax.user/1413 Regards, Edward On 13 March 2013 18:15, Edward d'Auvergne <[email protected]> wrote: > Hi, > > Have you tried Sebastien Morin's consistency testing analysis which is > in relax (http://www.nmr-relax.com/manual/Consistency_testing.html)? > This might tell you if there are problems with your relaxation data. > I would assume that you have used proper per-experiment temperature > calibration using MeOH/ethylene glycol and single-scan interleaving > for temperature control: > > http://www.nmr-relax.com/manual/Temperature_control_calibration.html > > And that you have used the appropriate spectral processing and peak > height extraction: > > http://www.nmr-relax.com/manual/From_spectra_peak_intensities_relaxation_rates.html > > These links are from the HTML version of the relax manual > (http://www.nmr-relax.com/manual/index.html). Note that the error > analysis is incredibly important - I always say that accuracy in the > errors is just as important, or maybe even more important, than the > data itself. If the errors are wrong, then the results from any type > of modelling analysis will be meaningless (there are shelves in maths > libraries dedicated to this large field of mathematics: > http://en.wikipedia.org/wiki/Mathematical_model) . > > Assuming you have done all of this, then there could be other issues > affecting the analysis. Did you collect all data on a single sample > and, if not, did you make sure the protein concentration was identical > in each sample? Partial dimerisation, even non-specific and at very > low percentages, could significantly affect the analysis. Even more > so if slightly different sample concentrations are used. Did you use > all of the global diffusion models in the model-free analysis? Are > the AIC values significantly different between the models? Also, did > you use relax to calculate the R1 and R2 relaxation rates and the NOE? > > Note that almost no protein will tumble as a perfect sphere. You can > see this with the inertia tensor, and almost no model-free analysis > using today's methodology will select the spherical tensor. One part > that you don't see, which is a very significant part of the diffusion > tensor, is the water shell. This can have different thicknesses > around your system depending upon surface > hydrophobicity/hydrophilicity, the presence of charges, bound metals > (even a loose attraction), and loop and other internal motions. So > even a perfect mathematical sphere with different localised surface > properties will not diffuse as a sphere. > > Anyway, I hope some of this information helps. > > Regards, > > Edward > > On 13 March 2013 17:31, Angelo Miguel Figueiredo > <[email protected]> wrote: >> 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 >>> <[email protected]> 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. >>>> >>>> _______________________________________________ >>>> relax (http://www.nmr-relax.com) >>>> >>>> This is the relax-users 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-users >>>> >> >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-users 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-users _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users 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-users
