Hi, Here is the partial result of sequence.display() command ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- relax> sequence.display(sep=None, mol_name_flag=True, res_num_flag=True, res_name_flag=True, spin_num_flag=True, spin_name_flag=True) # mol_name res_num res_name spin_num spin_name None 1 None None N None 2 None None N
Same is true for all the remaining residues. ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- I did run the dauvergne_protocol.py script. Thanks, Regards, lalit ________________________________________ From: [email protected] [[email protected]] On Behalf Of Edward d'Auvergne [[email protected]] Sent: Thursday, May 26, 2011 11:13 AM To: Deshmukh, Lalit (NIH/NIDDK) [F]; Michael Bieri Cc: [email protected] Subject: Re: problems with final_data_extraction.py Hi, Commenting out the lines might fix the problem. Could you nevertheless copy and paste the sequence information printed out by relax via the sequence.display() command. The missing diffusion tensor is interesting. How have you used relax? Have you used the new protocol of my paper http://www.nmr-relax.com/refs.html#dAuvergneGooley08b ? If so, maybe the local tm global model has been selected over the sphere, spheroids, and ellipsoid tensors. Can you see such a result from the relax printouts? Michael maybe able to better help out with these errors. Cheers, Edward On 26 May 2011 16:31, Deshmukh, Lalit (NIH/NIDDK) [F] <[email protected]> wrote: > Hi, > > Thanks for the reply. I've added "sequence.display()" and ran the script > again. Attached is the error file. > I also tried to modify the script (albeit crudely). Here are the > modifications: > ------------------------------------------------------------------------------------------------------------------------ > # spin_no = spin_id[spin_id.index(':')+1:spin_id.index('&')] > # spin_res = spin_id[spin_id.index('&')+2:spin_id.index('@')] > spin_no = spin_id[spin_id.index(':')+1:spin_id.index('@')] > spin_res = spin_no > print "spin_id is: X", spin_id, "X" > print "spin_no is: X", spin_no, "X" > self.file.write((spin_res) + " " + (spin_no)) > ------------------------------------------------------------------------------------------------------------------------- > # S2. > if hasattr(spin, 's2'): > s2 = str(spin.s2) > # s2_err = str(spin.s2_err) > if spin.s2 == None: > self.file.write("") > else: > # self.file.write(" " + s2[0:5]+ " +/- " + > s2_err[0:4]) > self.file.write(" " + s2[0:5]+ " +/- 0.00") > ------------------------------------------------------------------------------------------------------------------------ > # Rex. > if hasattr(spin, 'rex'): > rex = str(spin.rex) > # rex_err = str(spin.rex_err) > if spin.rex == None: > self.file.write("") > else: > # self.file.write(" " + rex[0:5]+ " +/- " > + rex_err[0:4]) > self.file.write(" " + rex[0:5]+ " +/- > 0.00") > -------------------------------------------------------------------------------------------------------------------------- > After these modifications, the script does create new directories > (final_results, grace, s2final_results) and writes all the files in it. > However, then fails with following message: > --------------------------------------------------------------------------------------------------------------------------- > relax> diffusion_tensor.display() > RelaxError: No diffusion tensor data exists. > ---------------------------------------------------------------------------------------------------------------------------- > > Thanks in advance, > > Regards, > Lalit > ________________________________________ > From: [email protected] [[email protected]] On Behalf Of > Edward d'Auvergne [[email protected]] > Sent: Thursday, May 26, 2011 4:30 AM > To: Deshmukh, Lalit (NIH/NIDDK) [F]; Michael Bieri > Cc: [email protected] > Subject: Re: problems with final_data_extraction.py > > Dear Lalit and Michael, > > Welcome to the relax mailing lists. I've looked into this and it > appears to be a problem in the script with the nomenclature of one of > your spin systems. Michael, would you be able to look into this? The > problem appear to be in the script. Lalit, it would help > significantly if you could provide some more information. With the > current information, we can see it is a problem with spin names. > However there is not enough info to pinpoint the problem. Would you > be able to give some more information? For example if you execute > "sequence.display()" prior to line 36 in the script, this will display > the sequence which might help with the debugging. > > Cheers, > > Edward > > > > ---------- Forwarded message ---------- > From: Deshmukh, Lalit (NIH/NIDDK) [F] <[email protected]> > Date: 23 May 2011 18:23 > Subject: problems with final_data_extraction.py > To: "[email protected]" <[email protected]> > > > Hi, > > I am having some trouble with final_data_extraction.py script. Here > is the error. > ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > relax> results.read(file='results', dir=None) > Opening the file 'results.bz2' for reading. > Traceback (most recent call last): > File "/usr/local/bin/relax", line 381, in <module> > Relax() > File "/usr/local/bin/relax", line 117, in __init__ > self.interpreter.run(self.script_file) > File "/usr/local/relax-1.3.10/prompt/interpreter.py", line 294, 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 "/usr/local/relax-1.3.10/prompt/interpreter.py", line 597, in run_script > return console.interact(intro, local, script_file, quit, > show_script=show_script, raise_relax_error=raise_relax_error) > File "/usr/local/relax-1.3.10/prompt/interpreter.py", line 483, in > interact_script > exec_script(script_file, local) > File "/usr/local/relax-1.3.10/prompt/interpreter.py", line 376, in > exec_script > runpy.run_module(module, globals) > File "/usr/lib/python2.6/runpy.py", line 140, in run_module > fname, loader, pkg_name) > File "/usr/lib/python2.6/runpy.py", line 34, in _run_code > exec code in run_globals > File > "/u/deshmukhl/Capsid/T1T1p_NOE/Relax/Calc/local_tm/aic/final_data_extraction.py", > line 36, in <module> > spin_no = spin_id[spin_id.index(':')+1:spin_id.index('&')] > ValueError: substring not found > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Thanks in advance, > > Regards, > Lalit > > _______________________________________________ > 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 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
