Re: Difficulty with noe.py sample script -- October 08, 2008 - 19:07

Yes, the standard deviation of the steady-state NOEs match to 15 
decimal places
(ignoring the occasional rounding error in excel).

The svn command definitely worked, and picked up a bunch of files, but the
updated software just didn't fix the problems (1.2.14 or 1.3.1 versions). But,
as you say, not all that important anymore since 1.2.12 is just fine for the
NOE.

Tyler


Quoting Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>:

> That's good to hear, that the values match.  I hope the errors match
> as well.  If subversion is installed, that then the only way that
> typing:
>
> svn co http://svn.gna.org/svn/relax/1.2 relax-1.2
>
> in a terminal can fail is if the Gna! (http://gna.org) open source
> infrastructure is down, which doesn't happen, or if the internet isn't
> working.  But if it's working for you, then you don't need to use SVN.
>
> Regards,
>
> Edward
>
>
>
> On Wed, Oct 8, 2008 at 3:46 PM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> > Of the suggested solutions only installing 1.2.12 and running noe.py from
> > that
> > actually seems to work. I installed a Mac OS X binary version of SVN, and it
> > seemed to work just fine, but maybe there's another build step or something
> > I
> > don't know about after using the commands outlined below. Anyways, the
> > steady-state NOE values from relax match perfectly with the parallel
> > calculations in excel, so that's good.
> >
> > Tyler
> >
> > Quoting Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>:
> >
> > > Hi,
> > >
> > > I've now found and fixed the bug in the 1.2 relax line (see
> > > https://gna.org/bugs/?12418).  I will release relax 1.2.15 with this
> > > fix soonish, but please be patient as it takes up to 6 solid hours to
> > > do a release.  If you can't wait, you have two alternatives.  The best
> > > would be to use the subversion program to get the most up-to-date copy
> > > of the 1.2 relax line by typing:
> > >
> > > $ svn co svn://svn.gna.org/svn/relax/1.2 relax-1.2
> > >
> > > or if this doesn't work:
> > >
> > > $ svn co http://svn.gna.org/svn/relax/1.2 relax-1.2
> > >
> > > Otherwise you could download and use relax.1.2.12.
> > >
> > > Regards,
> > >
> > > Edward
> > >
> > >
> > >
> > > On Tue, Oct 7, 2008 at 9:29 PM, Edward d'Auvergne
> > > <edward.dauvergne@xxxxxxxxx> wrote:
> > > > On Tue, Oct 7, 2008 at 7:48 PM, Tyler Reddy <TREDDY@xxxxxx> 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