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: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] On Behalf Of
Edward d'Auvergne [edward@xxxxxxxxxxxxx]
Sent: Thursday, May 26, 2011 4:30 AM
To: Deshmukh, Lalit (NIH/NIDDK) [F]; Michael Bieri
Cc: relax-users@xxxxxxx
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] <lalit.deshmukh@xxxxxxx>
Date: 23 May 2011 18:23
Subject: problems with final_data_extraction.py
To: "relax-users@xxxxxxx" <relax-users@xxxxxxx>
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
_______________________________________________
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_______________________________________________
relax (http://nmr-relax.com)
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relax-users@xxxxxxx
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RE: problems with final_data_extraction.py