On Tue, Oct 7, 2008 at 7:48 PM, Tyler Reddy <[EMAIL PROTECTED]> wrote:
> Hi Edward,
>
> Thanks for your continued patience.
That's okay, it's not a problem.
> Okay, it seems that aligning the data height column by the left most digit
> rather than the right most digit is not tolerated. Now the script (1.2)
> almost
> gets to the end, but there is still an error output, where the program opens
> noe.out for writing (see below). The noe.out file is created, but it's
> blank.
> Assuming I can get functional input for the 1.2 version (which is supposed
> to
> work), if this input doesn't work for the 1.3 version I'm happy to submit
> the
> bug report at that stage.
relax simply splits the text file by whitespace so alignment is only
an issue if columns fuse. I think there is another issue somewhere.
I've tried the analysis with some of my old data, but I get the
following error:
relax> calc(run='noe', print_flag=1)
relax> value.write(run='noe', param='noe', file='noe.out', dir=None, force=1)
Opening the file 'noe.out' for writing.
Traceback (most recent call last):
File "/data/relax/releases/relax-1.2.14/relax", line 457, in <module>
Relax()
File "/data/relax/releases/relax-1.2.14/relax", line 167, in __init__
self.interpreter.run()
File "/data/relax/releases/relax-1.2.14/prompt/interpreter.py", line
216, in run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File "/data/relax/releases/relax-1.2.14/prompt/interpreter.py", line
391, in run_script
console.interact(intro, local, script_file, quit)
File "/data/relax/releases/relax-1.2.14/prompt/interpreter.py", line
343, in interact_script
execfile(script_file, local)
File "noe.py", line 29, in <module>
value.write(name, param='noe', file='noe.out', force=1)
File "/data/relax/releases/relax-1.2.14/prompt/value.py", line 506, in write
self.__relax__.generic.value.write(run=run, param=param,
file=file, dir=dir, force=force)
File "/data/relax/releases/relax-1.2.14/generic_fns/value.py", line
537, in write
self.write_data(file, return_value)
File "/data/relax/releases/relax-1.2.14/generic_fns/value.py", line
549, in write_data
self.function_type =
self.relax.data.run_types[self.relax.data.run_names.index(run)]
ValueError: list.index(x): x not in list
This is exactly what you see. So I then tested this on many previous
relax releases and found that all versions up to 1.2.12 function
properly. This error is a regression which appeared in the 1.2.13
version and still exists in 1.2.14. So a temporary but quick fix
would be to do the NOE analysis using relax-1.2.12. For relaxation
curve fitting and model-free analysis, the 1.3.1 version can be used
(there are system tests for these analyses there so this is much less
likely to fail). I'm sorry if this caused inconveniences, I have no
idea how this error was introduced. I've created a bug report for
this issue (https://gna.org/bugs/index.php).
> Also, I think it would be very useful if a sample of functional input data,
> as
> you supplied for me in the previous email, would be incorporated in the
> relax
> manual. Different labs can have different naming conventions and formats,
> even
> within a Sparky list, and the column alignment can be tricky (even if
> trivial
> once you know about it). Also, if there is sensitivity to the nomenclature
> system employed (as some of your previous responses on this topic attest),
> then
> an example directly in the manual would definitely be appreciated. I know
> that
> part of the design philosophy is that it's very easy to incorporate new
> format
> tolerance into relax, but it's even faster for a new user who uses a
> slightly
> different format to just read the relevant section of the manual and format
> that way.
Done, I've added exactly the text you suggest
(https://mail.gna.org/public/relax-commits/2008-10/msg00079.html).
Thanks for the idea, that should be of help to others as well. Don't
worry about creating a bug report for relax-1.3.x as I'm now in the
process of creating a system test for the NOE analysis using a subset
of my old data.
Cheers,
Edward
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