Oh, if you have administrator slowness issues, this can easily be bypassed. See Christophe Fares' (cfares att uhnresearch dot ca) post at https://mail.gna.org/public/relax-users/2008-10/msg00052.html for details.
Regards, Edward On Thu, Nov 6, 2008 at 4:39 PM, Brosey, Chris A <[EMAIL PROTECTED]> wrote: > 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:[EMAIL PROTECTED] > Sent: Wed 11/5/2008 2:23 PM > To: Edward d'Auvergne > Cc: Brosey, Chris A; [email protected] > 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 <[EMAIL PROTECTED]>: > >> 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 <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]>: >>> >>>> 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 >>> [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 >> > > > > > _______________________________________________ relax (http://nmr-relax.com) This is the 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