Re: [relax-announce] relax version 4.1.3.
Hi Edward, indeed, no models have been selected for any of the residues. That might be, logically, the problem. This is the message I read after each of the nine attempted models: "RelaxWarning: No spins are selected therefore the optimisation or calculation cannot proceed." Suggestions? Stefano > On 12 Jul 2019, at 15:57, Edward d'Auvergne wrote: > > On Fri, 12 Jul 2019 at 15:16, Stefano Luciano Ciurli > wrote: >> >> Hi Edward, >> I hope I am sending the message to the correct address now. >> >> I think I have solved the issue that was causing the mentioned problem with >> the apparently incomplete set up by doing what you indicated. >> >> Now the calculation has gone for about 5 min with the following result: >> >> == >> = Completion of the d'Auvergne protocol model-free auto-analysis = >> == >> >> Elapsed time: 5 minutes and 54.350 seconds >> >> Exception raised in thread. >> >> Traceback (most recent call last): >> File "gui/analyses/execute.pyc", line 87, in run >> File "gui/analyses/auto_model_free.pyc", line 834, in run_analysis >> File "auto_analyses/dauvergne_protocol.pyc", line 249, in __init__ >> File "auto_analyses/dauvergne_protocol.pyc", line 610, in execute >> File "auto_analyses/dauvergne_protocol.pyc", line 855, in model_selection >> File "prompt/uf_objects.pyc", line 161, in __call__ >> File "pipe_control/model_selection.pyc", line 260, in select >> File "pipe_control/pipes.pyc", line 68, in bundle >> File "lib/checks.pyc", line 81, in __call__ >> RelaxNoPipeError: RelaxError: The data pipe 'aic - mf (Sun Jul 7 18:21:56 >> 2019)' has not been created yet. >> >> What should I make of it? > > Cheers! The error message has been seen before: > > > http://www.nmr-relax.com/mail.gna.org/public/relax-users/2012-11/msg5.html > > http://www.nmr-relax.com/mail.gna.org/public/relax-users/2008-11/msg00034.html > > However I've never had a bug report with enough details to reproduce > the problem to be able to catch it in the test suite. My guess is > that if you carefully look at the log messages (hopefully you ran it > with the log output to file), you'll see a series of RelaxWarning > messages earlier which explain the problem in detail. I would also > guess that no models have been select for one or more spin systems. > > Regards, > > Edward ___ nmr-relax-announce mailing list nmr-relax-announce@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nmr-relax-announce
Re: [relax-announce] relax version 4.1.3.
On Fri, 12 Jul 2019 at 15:16, Stefano Luciano Ciurli wrote: > > Hi Edward, > I hope I am sending the message to the correct address now. > > I think I have solved the issue that was causing the mentioned problem with > the apparently incomplete set up by doing what you indicated. > > Now the calculation has gone for about 5 min with the following result: > > == > = Completion of the d'Auvergne protocol model-free auto-analysis = > == > > Elapsed time: 5 minutes and 54.350 seconds > > Exception raised in thread. > > Traceback (most recent call last): > File "gui/analyses/execute.pyc", line 87, in run > File "gui/analyses/auto_model_free.pyc", line 834, in run_analysis > File "auto_analyses/dauvergne_protocol.pyc", line 249, in __init__ > File "auto_analyses/dauvergne_protocol.pyc", line 610, in execute > File "auto_analyses/dauvergne_protocol.pyc", line 855, in model_selection > File "prompt/uf_objects.pyc", line 161, in __call__ > File "pipe_control/model_selection.pyc", line 260, in select > File "pipe_control/pipes.pyc", line 68, in bundle > File "lib/checks.pyc", line 81, in __call__ > RelaxNoPipeError: RelaxError: The data pipe 'aic - mf (Sun Jul 7 18:21:56 > 2019)' has not been created yet. > > What should I make of it? Cheers! The error message has been seen before: http://www.nmr-relax.com/mail.gna.org/public/relax-users/2012-11/msg5.html http://www.nmr-relax.com/mail.gna.org/public/relax-users/2008-11/msg00034.html However I've never had a bug report with enough details to reproduce the problem to be able to catch it in the test suite. My guess is that if you carefully look at the log messages (hopefully you ran it with the log output to file), you'll see a series of RelaxWarning messages earlier which explain the problem in detail. I would also guess that no models have been select for one or more spin systems. Regards, Edward ___ nmr-relax-announce mailing list nmr-relax-announce@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nmr-relax-announce
Re: [relax-announce] relax version 4.1.3.
Hi Edward, I hope I am sending the message to the correct address now. I think I have solved the issue that was causing the mentioned problem with the apparently incomplete set up by doing what you indicated. Now the calculation has gone for about 5 min with the following result: == = Completion of the d'Auvergne protocol model-free auto-analysis = == Elapsed time: 5 minutes and 54.350 seconds Exception raised in thread. Traceback (most recent call last): File "gui/analyses/execute.pyc", line 87, in run File "gui/analyses/auto_model_free.pyc", line 834, in run_analysis File "auto_analyses/dauvergne_protocol.pyc", line 249, in __init__ File "auto_analyses/dauvergne_protocol.pyc", line 610, in execute File "auto_analyses/dauvergne_protocol.pyc", line 855, in model_selection File "prompt/uf_objects.pyc", line 161, in __call__ File "pipe_control/model_selection.pyc", line 260, in select File "pipe_control/pipes.pyc", line 68, in bundle File "lib/checks.pyc", line 81, in __call__ RelaxNoPipeError: RelaxError: The data pipe 'aic - mf (Sun Jul 7 18:21:56 2019)' has not been created yet. What should I make of it? Stefano > On 12 Jul 2019, at 09:22, Edward d'Auvergne wrote: > > On Sun, 7 Jul 2019 at 18:37, Stefano Luciano Ciurli > wrote: >> >> Hi Edward, >> >> thank you for this update. The previous problems are solved now! >> >> Proceeding further, and having loaded spins from a PDB structure which >> includes, of course, H and N nuclei, I receive a message when executing the >> program that says that the set up is incomplete, and that interatomic data >> for the dipole-dipole interaction is missing, followed by the full list of N >> and H atoms for each residue in the protein sequence. >> >> Also, it suggests to try the “spin-isotope user function”. >> >> What should I do? > > Hi Stefano, > > It took a while for your message to get through as you emailed the > relax announcement mailing list. I've now changed the address for > this email thread to the relax users mailing list. I have configured > the relax announcement list to set the explicit "Reply-To:" header to > the users mailing list. Could you please deactivate the setting in > your email software that is causing this to be ignored? This > "Reply-To:" header is also used for the commits mailing list to direct > those responses to the development mailing list. The announcement and > commit mailing lists are read-only. > > For this "The set up is incomplete. Please check for the following > missing information: Interatomic data (for the dipole-dipole > interaction)" issue, have you clicked on all of the buttons under the > relaxation data list GUI element? You need to click on each one of > these buttons to complete the set up. Note that these are > deliberately not mandatory, as people with corner case molecular > systems will sometimes instead use the user function menus to set up > their non-standard spin systems. > > Regards, > > Edward ___ nmr-relax-announce mailing list nmr-relax-announce@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nmr-relax-announce
Re: [relax-announce] relax version 4.1.3.
On Sun, 7 Jul 2019 at 18:37, Stefano Luciano Ciurli wrote: > > Hi Edward, > > thank you for this update. The previous problems are solved now! > > Proceeding further, and having loaded spins from a PDB structure which > includes, of course, H and N nuclei, I receive a message when executing the > program that says that the set up is incomplete, and that interatomic data > for the dipole-dipole interaction is missing, followed by the full list of N > and H atoms for each residue in the protein sequence. > > Also, it suggests to try the “spin-isotope user function”. > > What should I do? Hi Stefano, It took a while for your message to get through as you emailed the relax announcement mailing list. I've now changed the address for this email thread to the relax users mailing list. I have configured the relax announcement list to set the explicit "Reply-To:" header to the users mailing list. Could you please deactivate the setting in your email software that is causing this to be ignored? This "Reply-To:" header is also used for the commits mailing list to direct those responses to the development mailing list. The announcement and commit mailing lists are read-only. For this "The set up is incomplete. Please check for the following missing information: Interatomic data (for the dipole-dipole interaction)" issue, have you clicked on all of the buttons under the relaxation data list GUI element? You need to click on each one of these buttons to complete the set up. Note that these are deliberately not mandatory, as people with corner case molecular systems will sometimes instead use the user function menus to set up their non-standard spin systems. Regards, Edward ___ nmr-relax-announce mailing list nmr-relax-announce@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/nmr-relax-announce
