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From: Brosey, C. A <chr...@do...> - 2008-11-06 16:44:41
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Many thanks for the quick responses. I have already updated relax using subversion as you recommended and am awaiting installation of the minfx library from my system administrator. The error still occurs with just the relax update alone, so hopefully things will resolve once the library is in place. I will keep you posted. Regards, Chris -----Original Message----- From: Tyler Reddy [mailto:TR...@DA...] Sent: Wed 11/5/2008 2:23 PM To: Edward d'Auvergne Cc: Brosey, Chris A; rel...@do... Subject: Re: Writing/displaying output from full_analysis.py Since I've been setting up relax on other machines I also remembered that you will have problems if you don't get the latest build of minfx by going into the directory for minfx and using subversion: svn co svn://svn.gna.org/svn/minfx/trunk minfx (and then all further updates can be done with svn up, as Edward says) Also, for minfx, don't forget to actually install the new version. You have to change directory to the nested minfx folder and run python setup.py install Tyler Quoting Edward d'Auvergne <edw...@do...>: > Cheers! That response pretty much covers it. I'm not sure if this is > exactly the error I fixed for you Tyler, but I think the repository > version doesn't have this problem. It would be useful to get the > repository version anyway as then the debugged version will be > instantly acessable by typing: > > $ svn up > > in the directory of the checked out copy. I can't guarantee a quick > response time though as RSI in my wrist is slowing things down > significantly - writing an email only with my left hand is hard > enough, and debugging one handed would be a nightmare! > > Regards, > > Edward > > > On Wed, Nov 5, 2008 at 8:03 PM, Tyler Reddy <TR...@da...> wrote: >> For the sequence input file I think you want Spin_Name to be N if >> this is 15N >> relaxation data. I'm also thinking it's not a bad idea to update to >> the latest >> build of relax using subversion (can easily find/download this software via >> google). This looks vaguely similar to some of the problems Edward had >> debugged >> for me, so probably worth the time to update if you're going to use this >> script. >> >> The command to execute in the relax directory would be: >> >> svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3 >> >> And then a newer version of relax is put in a nested folder in the relax >> directory. You want to make sure that the system path refers to the >> newer build >> of relax instead of the one you originally downloaded. When you type >> 'relax' it >> should say something like 'system repository checkout' instead of 'relax >> 1.3.2.' >> >> So the new directory would be ../relax-1.3.2/relax-1.3 >> >> Edward will probably have a more effective response, but this stuff will >> probably prevent other problems in any case. >> >> Tyler >> >> >> Quoting "Brosey, Chris A" <chr...@do...>: >> >>> Greetings, >>> >>> I have encountered a problem running the script full_analysis.py >>> using v1.3.2 of relax (and python v2.5). I am currently executing >>> the script with the MI option (DIFF_MODEL = 'local_tm'). I find that >>> the script successfully reads in data files and carries out the grid >>> search and minimization specified under the multi_model function for >>> the very first 'tm0' model. However, it appears that there is a >>> problem executing the final command of the function - writing the >>> results to an output file (see reproduction of log file and traceback >>> below). The proper directory and file are created, but the 'results' >>> file remains empty; and the script returns the error message >>> 'IndexError: list index out of range'. >>> >>> I obtain the same error using various formatted versions of my own >>> data files, as well as the test data files found in >>> /test_suite/shared_data/model_free/S2_0..0.149/, modified to include >>> None for data values of GLY 1. Running multi_model commands manually >>> through the relax prompt also returns the same error for both >>> 'results.write' and 'results.display.' I also obtain the same result >>> running the analysis with sample_scripts/model-free.py. >>> >>> I am new to python and the relax interface and apologize if I am >>> bringing up a very basic question. I appreciate any help and >>> suggestions you might have. Thanks! >>> >>> Regards, >>> >>> Chris >>> >>> >>> Log File (edited) >>> >>> relax> pipe.create(pipe_name='tm0', pipe_type='mf') >>> >>> relax> sequence.read(file='noe.500.out', >>> dir='~/relax/relax-1.3.2/sample_scripts/data', mol_name_col=None, >>> res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, >>> sep=None) >>> Opening the file >>> '/home/broseyca/relax/relax-1.3.2/sample_scripts/data/noe.500.out' >>> for reading. >>> Mol_name Res_num Res_name Spin_num Spin_name >>> None 1 GLY None None >>> None 2 ALA None None >>> >>> relax> relax_data.read(ri_label='R1', frq_label='500', >>> frq=500100000.0, file='r1.500.out', >>> dir='~/relax/relax-1.3.2/sample_scripts/data', mol_name_col=None, >>> res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, >>> data_col=2, error_col=3, sep=None) >>> Opening the file >>> '/home/broseyca/relax/relax-1.3.2/sample_scripts/data/r1.500.out' for >>> reading. >>> >>> #(A total of 6 relaxation files were read in). >>> >>> relax> model_free.select_model(model='tm0', spin_id=None) >>> >>> relax> grid_search(lower=None, upper=None, inc=11, constraints=True, >>> verbosity=1) >>> >>> relax> minimise(*args=('newton',), func_tol=1e-25, >>> max_iterations=10000000, constraints=True, scaling=True, verbosity=1) >>> >>> relax> results.write(file='results', dir='local_tm/tm0', force=True, >>> format='xml', compress_type=1) >>> Opening the file 'local_tm/tm0/results.bz2' for writing. >>> >>> >>> Traceback Message >>> >>> 77 sweet:/home/broseyca/relax/relax-1.3.2% Traceback (most recent >>> call last): >>> File "relax", line 410, in <module> >>> Relax() >>> File "relax", line 127, in __init__ >>> self.interpreter.run(self.script_file) >>> File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line >>> 270, 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 "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line >>> 531, in run_script >>> return console.interact(intro, local, script_file, quit, >>> show_script=show_script, raise_relax_error=raise_relax_error) >>> File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line >>> 427, in interact_script >>> execfile(script_file, local) >>> File "prompt/full_analysis2.py", line 668, in <module> >>> Main(self.relax) >>> File "prompt/full_analysis2.py", line 221, in __init__ >>> self.multi_model(local_tm=True) >>> File "prompt/full_analysis2.py", line 664, in multi_model >>> results.write(file='results', dir=dir, force=True) >>> File "/home/broseyca/relax/relax-1.3.2/prompt/results.py", line 173, >>> in write >>> results.write(file=file, directory=dir, force=force, >>> format=format, compress_type=compress_type) >>> File "/home/broseyca/relax/relax-1.3.2/generic_fns/results.py", line >>> 164, in write >>> write_function(results_file) >>> File "/home/broseyca/relax/relax-1.3.2/data/__init__.py", line 222, >>> in to_xml >>> self[self.current_pipe].to_xml(self.xmldoc, pipe_element) >>> File "/home/broseyca/relax/relax-1.3.2/data/pipe_container.py", line >>> 234, in to_xml >>> self.mol.to_xml(doc, element) >>> File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line >>> 690, in to_xml >>> self[i].res.to_xml(doc, mol_element) >>> File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line >>> 492, in to_xml >>> self[i].spin.to_xml(doc, res_element) >>> File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line >>> 242, in to_xml >>> desc = return_data_desc(name, spin=self[i]) >>> File >>> "/home/broseyca/relax/relax-1.3.2/specific_fns/model_free/main.py", >>> line 2082, in return_data_desc >>> rex_units = self.return_units('rex', spin=spin) >>> File >>> "/home/broseyca/relax/relax-1.3.2/specific_fns/model_free/main.py", >>> line 2285, in return_units >>> return spin.frq_labels[0] + ' MHz' >>> IndexError: list index out of range >>> >>> >>> >>> >> >> >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-users mailing list >> rel...@do... >> >> 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 > rel...@do... > > 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 > |
