Hi Daniel, Don't worry about what I said about the diffusion tensor. I was just changing some diffusion tensor input code at the time, but the full_analysis.py doesn't use this anyway. It should be perfectly fine to use the code as is.
Regards, Edward 2010/3/17 Edward d'Auvergne <[email protected]>: > Hi, > > The trick here is to have a look at the new full_analysis.py sample > script. This has changed quite a lot since relax-1.3.4. Most of the > script has been shifted into the core of relax. Nevertheless you > should be able to quite easily modify the new script to perform your > analysis. There is something that will change soon with the diffusion > tensor in the 1.3 repository line, so I'll tell you hopefully today > how to get the change ('svn up' in the relax base directory). > > Regards, > > Edward > > > > 2010/3/17 Daniel Pérez <[email protected]>: >> Hi Edward, >> thanks for your quick answer. >> I download the latest of relax 1.3 using >> >> $ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3 >> >> Now when I run full_analysis.py with it I get the following error message >> >> Traceback (most recent call last): >> File "/soft/group/relax/relax-1.3/relax", line 358, in ? >> Relax() >> File "/soft/group/relax/relax-1.3/relax", line 126, in __init__ >> self.interpreter.run(self.script_file) >> File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 287, in run >> return run_script(intro=self.__intro_string, local=locals(), >> script_file=script_file, quit=self.__quit_flag, >> show_script=self.__show_script, raise_relax_error=self.__raise_relax_error) >> File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 533, in >> run_script >> return console.interact(intro, local, script_file, quit, >> show_script=show_script, raise_relax_error=raise_relax_error) >> File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 429, in >> interact_script >> execfile(script_file, local) >> File "full_analysis.py", line 674, in ? >> Main(self.relax) >> AttributeError: Interpreter instance has no attribute 'relax' >> >> >> It looks like a pretty basic error, but still I'm stacked with it >> Regards >> Daniel >> >> >> Dr. Daniel Pérez >> Institut für Molekularbiologie und Biophysik >> Schafmattstrasse 20 >> ETH-Hönggerberg, HPK G 5 >> CH-8093 Zürich >> Phone: +41 44 633 25 37 >> E-mail: [email protected] >> Dr. Daniel Pérez >> Institut für Molekularbiologie und Biophysik >> Schafmattstrasse 20 >> ETH-Hönggerberg, HPK G 5 >> CH-8093 Zürich >> Phone: +41 44 633 25 37 >> E-mail: [email protected] >> On Mar 17, 2010, at 9:58 AM, Edward d'Auvergne wrote: >> >> Hi Daniel, >> >> This is actually a bug that was fixed a while ago >> (http://gna.org/bugs/?15050). I have to release relax-1.3.5 soon as >> there are many bug fixes in the repository sitting there waiting. If >> you can't wait, you can obtain the new code by following the >> instructions in one of the following: >> >> https://mail.gna.org/public/relax-users/2008-09/msg00002.html >> https://mail.gna.org/public/relax-users/2008-10/msg00013.html >> https://mail.gna.org/public/relax-users/2006-11/msg00006.html >> >> All the links are to help with Google indexing, just like this >> http://www.nmr-relax.com/ ;) The first should be enough, but the >> others might give more info if you need it. >> >> Regards, >> >> Edward >> >> >> >> 2010/3/17 Daniel Pérez <[email protected]>: >> >> Hi Edward, >> >> I hope you have some time to take a look at this. I have a data set at two >> fields. I used relax for fitting the data, but when and run the >> full_analysis script, after the software starts the grid search I get the >> following error message >> >> Traceback (most recent call last): >> >> File "/soft/group/relax/relax-1.3.4/relax", line 418, in ? >> >> Relax() >> >> File "/soft/group/relax/relax-1.3.4/relax", line 127, in __init__ >> >> self.interpreter.run(self.script_file) >> >> File "/soft/group/relax/relax-1.3.4/prompt/interpreter.py", line 276, in >> run >> >> return run_script(intro=self.__intro_string, local=self.local, >> script_file=script_file, quit=self.__quit_flag, >> show_script=self.__show_script, raise_relax_error=self.__raise_relax_error) >> >> File "/soft/group/relax/relax-1.3.4/prompt/interpreter.py", line 537, in >> run_script >> >> return console.interact(intro, local, script_file, quit, >> show_script=show_script, raise_relax_error=raise_relax_error) >> >> File "/soft/group/relax/relax-1.3.4/prompt/interpreter.py", line 433, in >> interact_script >> >> execfile(script_file, local) >> >> File "full_analysis_markup.py", line 764, in ? >> >> Main(self.relax) >> >> File "full_analysis_markup.py", line 226, in __init__ >> >> self.multi_model(local_tm=True) >> >> File "full_analysis_markup.py", line 755, in multi_model >> >> grid_search(inc=GRID_INC) >> >> File "/soft/group/relax/relax-1.3.4/prompt/minimisation.py", line 156, in >> grid_search >> >> minimise.grid_search(lower=lower, upper=upper, inc=inc, >> constraints=constraints, verbosity=verbosity) >> >> File "/soft/group/relax/relax-1.3.4/generic_fns/minimise.py", line 191, in >> grid_search >> >> grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints, >> verbosity=verbosity) >> >> File >> "/soft/group/relax/relax-1.3.4/specific_fns/model_free/mf_minimise.py", line >> 479, in grid_search >> >> self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, >> constraints=constraints, verbosity=verbosity, sim_index=sim_index) >> >> File >> "/soft/group/relax/relax-1.3.4/specific_fns/model_free/mf_minimise.py", line >> 789, in minimise >> >> model_type = self.determine_model_type() >> >> File "/soft/group/relax/relax-1.3.4/specific_fns/model_free/main.py", line >> 1015, in determine_model_type >> >> if cdp.diff_tensor.fixed: >> >> AttributeError: 'PipeContainer' object has no attribute 'diff_tensor' >> >> >> Checking the mailing archive I saw that Tiago Pais got the same error >> message last year. >> >> That time you suggested him to use a script containing a markup: >> >> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/full_analysis.py?rev=9794&view=markup >> >> ( >> >> The complete answer was: >> >> Re: Error when running full_analysis.py script >> >> Edward d'Auvergne >> >> Tue, 27 Oct 2009 03:02:16 -0700 >> >> Dear Tiago, >> >> This is a hard one to catch. I have just added a function to this >> >> script to check the validity of the user variables >> >> (http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/full_analysis.py?rev=9794&view=markup). >> >> This should give better error messages specifically identifying the >> >> problem. For this second issue you are having, it is a little hard to >> >> see what the problem is. Would you be able to supply a little more >> >> information. For example the version of relax you are using, the full >> >> error message, how you have executed the full_analysis.py script and >> >> at what stage you are up to, etc. With more information, I should be >> >> able to track down the issue. >> >> Cheers, >> >> Edward >> >> ) >> >> >> >> The traceback I showed to you above is coming from running that script, I >> got the same error message when I run the canonical full_analysis script. >> >> I'm running relax 1.3.4 in RHEL distribution 5.1.19.6, kernel /vmlinuz >> 2.6.18-128.1.10.e15 >> >> It will be nice if you can help me with this >> >> Best regards >> >> Daniel >> >> >> >> Dr. Daniel Pérez >> >> Institut für Molekularbiologie und Biophysik >> >> Schafmattstrasse 20 >> >> ETH-Hönggerberg, HPK G 5 >> >> CH-8093 Zürich >> >> Phone: +41 44 633 25 37 >> >> E-mail: [email protected] >> >> >> _______________________________________________ >> >> relax (http://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://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
