Re: [sr #3195] Fitting of saturation recovery experiment -- November 29, 2014 - 17:11

Hi Andras,

If you update relax and recompile the C modules:

$ svn up
$ scons clean_all
$ scons

Then run your system test:

$ relax -sd Relax_fit.test_saturation_recovery

You should now see that the test passes.  I have implemented the
saturation recovery equations, gradients, and Hessians in the new
target_functions/exponential_sat.c file.  If you would like to create
Sparky files for the inversion recovery experiment, where I0 < Iinf, I
could do the same thing for this curve type as well.

Cheers,

Edward




On 29 November 2014 at 16:58, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Hi Andras,
>
> I've now added this:
>
> - The script has been added
> (http://article.gmane.org/gmane.science.nmr.relax.scm/24570).
> - Modified the script to work as a system test
> (http://article.gmane.org/gmane.science.nmr.relax.scm/24572).
> - Updated the copyright notice with your name
> (http://article.gmane.org/gmane.science.nmr.relax.scm/24574).
> - Created the system test
> (http://article.gmane.org/gmane.science.nmr.relax.scm/24575).
>
> Your script can now be run by typing:
>
> $ relax -sd Relax_fit.test_saturation_recovery
>
> Regards,
>
> Edward
>
>
>
> On 29 November 2014 at 15:23, Boeszoermenyi, Andras
> <Andras_Boeszoermenyi@xxxxxxxxxxxxxxx> wrote:
> > Dear Edward,
> >
> > thanks a lot for the great explanations.
> >
> > Unfortunately, I cannot figure out, what to paste where and rename to what.
> >
> > I won't feel offended though, if you implement it.
> >
> > Best,
> > Andras
> > ________________________________________
> > From: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] On Behalf Of 
> > Edward d'Auvergne [edward@xxxxxxxxxxxxx]
> > Sent: Friday, November 28, 2014 1:24 PM
> > To: Boeszoermenyi, Andras
> > Cc: relax-devel@xxxxxxx; Sébastien M
> > Subject: Re: [sr #3195] Fitting of saturation recovery experiment
> >
> > Hi Andras,
> >
> > To push changes into the source code repository, you'd have to become
> > a relax developer.  If you are interested, I'd recommend first reading
> > of the 'open source infrastructure' and 'relax development' chapters
> > of the manual.  These chapters outline the procedure in full detail.
> > Do you have experience with CVS, subversion, git, or other source code
> > revision control systems?
> >
> > The first step to have changes made to relax is to upload either files
> > or patches to a relax task, and ask for it to be included or applied.
> > For example I could take the script you have just attached to the task
> > in the 'saturation_recovery.tar.gaz' file (https://gna.org/task/?7415,
> > https://gna.org/task/download.php?file_id=22997), and place this into
> > the relax system test directories.  However, if you feel adventurous,
> > you could try to create your own system test from this!  I could then
> > incorporate your self designed test and add this to relax.  Creating
> > this test is rather straight forward:
> >
> >
> > - Firstly you will need a copy of the relax trunk in your home
> > directory that you can modify yourself.  The /sw/lib/ version is no
> > good for this.
> >
> >
> > - Copy your script to the new file
> > test_suite/system_tests/scripts/relax_fit_saturation_recovery.py.  Add
> > this to the repository by typing:
> >
> > $ svn add test_suite/system_tests/scripts/relax_fit_saturation_recovery.py
> >
> > You can then see the status of the relax source code by typing:
> >
> > $ svn st
> >
> > which will show your newly added script.
> >
> >
> > - The next step would be to add a copyright notice.  Open any relax
> > *.py file and copy the notice from the top into your script.  Remove
> > all authors and place your name and the year there.  You could also
> > include the link to your Gna! profile in brackets after your name
> > (https://gna.org/users/andras).
> >
> >
> > - Then to create the test itself.  I would suggest that this is called
> > Relax_fit.test_saturation_recovery.  Open the
> > test_suite/system_tests/relax_fit.py in a text editor (preferably
> > something such as gvim or emacs where source code is recognised, and
> > coloured, and the programs help you with the code).  Copy the 11 lines
> > of the test_zooming_grid_search() method
> > (http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_fit-pysrc.html#Relax_fit.test_zooming_grid_search)
> > and paste and rename it to test_saturation_recovery().  Be sure that
> > alphabetical order is preserved.  Change the script name to your
> > script, and the chi-squared value to 0.0, and the I0 and Rx values to
> > your values.  As you are changing this file, add a new line to the
> > copyright notice with your name and the year.
> >
> >
> > - Try running the test with:
> >
> > $ relax -s Relax_fit.test_saturation_recovery
> >
> >
> > - This will probably not run straight away, as you need to fix the
> > paths in the script.  Open your script and the
> > test_suite/system_tests/scripts/relax_fit_zooming_grid.py script
> > side-by-side (run 'svn up' now as I just simplified this reference
> > script for you).  Note the use of the relax status object (used to
> > find where relax is installed) and the os.sep Python module to support
> > all operating systems, as '/' in Windows is '\' (fortunately Macs
> > don't use ':' as a folder separator any more).  After this the test
> > should run and be complete.  Yet it will fail due to the chi-squared
> > and parameter check, and because the saturation-recovery equations are
> > not implemented yet.
> >
> >
> > - Finally prepare a patch by typing:
> >
> > $ svn diff > patch
> >
> > This will contain all the changes, including the new script file.
> > Upload the 'patch' file to the task, remembering to add a comment
> > describing the patch.  You may even wish to create your own commit
> > message - see the development chapter.
> >
> >
> > - Code review.  I'll look at the patch and make suggestions for
> > improvements.  Changes can be made and a new patch created and
> > uploaded.
> >
> >
> > - Once the patch is in a good state,  I can apply it to the relax
> > trunk and permanently commit the change to the repository.
> >
> >
> > This is essentially the starting procedure for becoming a developer.
> > Many more details are given in the development chapter.  The reason
> > I'm mentioning all of this now is because it's 7 pm Friday evening
> > here and I won't have a chance to look at this until next week.  For
> > me, creating this test is less than 5 min of work.  If you have the
> > interest, feel free to try it out yourself.
> >
> > Regards,
> >
> > Edward
> >
> >
> > P. S.  As for deleting files, this is not possible.  The
> > infrastructure that relax uses, and open source infrastructure in
> > general, is deliberately designed so that everything is permanent.
> >
> >
> >
> > On 28 November 2014 at 18:38, Boeszoermenyi, Andras
> > <Andras_Boeszoermenyi@xxxxxxxxxxxxxxx> wrote:
> > > Hi,
> > >
> > > great, this really helped.
> > >
> > > The script runs now for exponential fitting 'exp' and throws an error for 
> > > inversion recovery fitting 'inv'.
> > >
> > > I uploaded a new saturation recovery folder:
> > >
> > > file #22997:  saturation_recovery.tar.gaz
> > >
> > > Is there a way to remove the old one? And is there a way for me to push 
> > > changes through svn?
> > >
> > > Best,
> > > Andras
> > > ____________________________
> > > From: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] On Behalf 
> > > Of Edward d'Auvergne [edward@xxxxxxxxxxxxx]
> > > Sent: Friday, November 28, 2014 12:16 PM
> > > To: Boeszoermenyi, Andras
> > > Cc: relax-devel@xxxxxxx; Sébastien M
> > > Subject: Re: [sr #3195] Fitting of saturation recovery experiment
> > >
> > > Hi,
> > >
> > > Ok, then you're almost there.  You'll need to obtain a copy of minfx
> > > (https://gna.org/projects/minfx/) and bmrblib
> > > (https://gna.org/projects/bmrblib/).  These used to be relax packages,
> > > but they have been spun out into their own for others to take
> > > advantage of.  For this, type:
> > >
> > > $ cd /sw/lib/relax-trunk/
> > > $ svn co http://svn.gna.org/svn/minfx/tags/1.0.11/minfx
> > > $ svn co http://svn.gna.org/svn/bmrblib/tags/1.0.3/bmrblib
> > >
> > > This is performed when a new relax release is made so that minfx and
> > > bmrblib are bundled with relax, but this needs to be performed
> > > manually when using the most cutting edge code.  Note that it is much
> > > better to place the relax-trunk into your home directory as this will
> > > be constantly modified by the relax developers.  Then, as a normal
> > > user (without sudo), you can obtain the latest code by typing:
> > >
> > > $ svn up
> > >
> > > Regards,
> > >
> > > Edward
> > >
> > >
> > > P. S.  The command for showing the PATH environmental variable is
> > > "echo $PATH" rather than just "$PATH".
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On 28 November 2014 at 18:07, Boeszoermenyi, Andras
> > > <Andras_Boeszoermenyi@xxxxxxxxxxxxxxx> wrote:
> > > > Hi,
> > > >
> > > > so I aliased relax to the trunk relax and can start it now, but here is 
> > > > the problem:
> > > >
> > > >  File "/sw/lib/relax-trunk/relax", line 4, in <module>
> > > >     import relax
> > > >   File "/sw/lib/relax-trunk/relax.py", line 37, in <module>
> > > >     import dep_check
> > > >   File "/sw/lib/relax-trunk/dep_check.py", line 90, in <module>
> > > >     if not minfx.__version__ == 'trunk' and 
> > > > version_comparison(minfx.__version__, min_version) == -1:
> > > > AttributeError: 'module' object has no attribute '__version__'
> > > >
> > > > which relax now gives:
> > > >
> > > > which relax
> > > > relax:   aliased to /sw/lib/relax-trunk/relax
> > > >
> > > > and $PATH:
> > > >
> > > > /sw/bin:/sw/sbin:.:/Applications/NMRpipe/nmrbin.mac:/Applications/NMRpipe/com:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/xplor-nih-2.33/bin:/opt/X11/bin:
> > > >  Command not found.
> > > >
> > > >
> > > > The locations are:
> > > >
> > > > /sw/lib/relax-py27/relax_gui_mode.py
> > > > /sw/lib/relax-py27/relax_gui_mode.pyo
> > > > /sw/lib/relax-trunk/relax_gui_mode.py
> > > >
> > > > I installed relax previously with fink. Unfortunately, fink does't 
> > > > support yosemite yet, so I can't install newer versions this way, except 
> > > > for the app.
> > > >
> > > > Best regards,
> > > > Andras
> > > > ________________________________________
> > > > From: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] On Behalf 
> > > > Of Edward d'Auvergne [edward@xxxxxxxxxxxxx]
> > > > Sent: Friday, November 28, 2014 11:46 AM
> > > > To: Boeszoermenyi, Andras
> > > > Cc: relax-devel@xxxxxxx; Sébastien M
> > > > Subject: Re: [sr #3195] Fitting of saturation recovery experiment
> > > >
> > > > Hi,
> > > >
> > > > Hmmm, this might be difficult to work out due to the number of
> > > > possibilities (Fink, Homebrew, framework installs, standard installs,
> > > > etc.).  So I'd need a bit more information.  Which method did you use
> > > > to obtain the code for the relax trunk?  Do you have Xcode, Scons,
> > > > subversion, Python, etc. installed all via DMG packages?  How did you
> > > > install relax to start with?  Are you the administrator for your
> > > > computer?  To find the different relax installations, maybe type:
> > > >
> > > > $ sudo /usr/libexec/locate.updatedb
> > > > $ locate relax_gui_mode.py
> > > >
> > > > Could you copy and paste the output of this into a mail?  This should
> > > > find all places where relax is located (the relax_gui_mode.py script
> > > > is simply a unique file name).  Then to find out where the default
> > > > relax is, type:
> > > >
> > > > $ which relax
> > > >
> > > > This will be the version that runs when you type 'relax'.  If you have
> > > > the relax trunk in the ~/relax-trunk directory (where ~ is your home
> > > > directory), then to run this version type:
> > > >
> > > > $ ~/relax-trunk/relax
> > > >
> > > > Does this work for you?  You can sometimes override the version
> > > > installed in /usr/local/ by creating a 'bin' directory and linking the
> > > > main relax file:
> > > >
> > > > $ cd ~
> > > > $ mkdir bin
> > > > $ cd bin
> > > > $ ln -s ~/relax-trunk/relax
> > > > $ cd
> > > > $ which relax
> > > >
> > > > Replace "~/relax-trunk" with any path you wish.  Normally ~/bin will
> > > > come before /usr/local in your $PATH environmental variable.  To be
> > > > sure, could you tell me what you see when you type:
> > > >
> > > > $ echo $PATH
> > > >
> > > > Note that in all of the above commands, that the '$ ' is the terminal
> > > > or prompt and that you should not type this.
> > > >
> > > > Regards,
> > > >
> > > > Edward
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On 28 November 2014 at 17:30, Boeszoermenyi, Andras
> > > > <Andras_Boeszoermenyi@xxxxxxxxxxxxxxx> wrote:
> > > > > Hi,
> > > > >
> > > > > would you happen to know where all these things install themselfes to. 
> > > > > I am at a complete loss.
> > > > >
> > > > > Best,
> > > > > Andras
> > > > > ________________________________________
> > > > > From: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] On Behalf 
> > > > > Of Edward d'Auvergne [edward@xxxxxxxxxxxxx]
> > > > > Sent: Friday, November 28, 2014 9:53 AM
> > > > > To: Boeszoermenyi, Andras
> > > > > Cc: relax-devel@xxxxxxx; Sébastien M
> > > > > Subject: Re: [sr #3195] Fitting of saturation recovery experiment
> > > > >
> > > > > Hi,
> > > > >
> > > > > Somehow the relax-trunk version is not located on the system path or
> > > > > it doesn't have priority over the installed 3.1.7 version.  You could
> > > > > supply the full path to override this, uninstall the 3.1.7 version, or
> > > > > change the order of the directories in the $PATH environmental
> > > > > variable.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Edward
> > > > >
> > > > >
> > > > >
> > > > > On 28 November 2014 at 15:47, Boeszoermenyi, Andras
> > > > > <Andras_Boeszoermenyi@xxxxxxxxxxxxxxx> wrote:
> > > > > > Well I installed the relax-trunk version, but I am not sure if that is 
> > > > > > what I am running.
> > > > > >
> > > > > > When I type relax -i
> > > > > >
> > > > > > I get this header:
> > > > > >
> > > > > > relax 3.1.7
> > > > > >
> > > > > >                               Molecular dynamics by NMR data analysis
> > > > > >
> > > > > >                              Copyright (C) 2001-2006 Edward d'Auvergne
> > > > > >                          Copyright (C) 2006-2014 the relax development 
> > > > > > team
> > > > > >
> > > > > > This is free software which you are welcome to modify and redistribute 
> > > > > > under the conditions of the
> > > > > > GNU General Public License (GPL).  This program, including all 
> > > > > > modules, is licensed under the GPL
> > > > > > and comes with absolutely no warranty.  For details type 'GPL' within 
> > > > > > the relax prompt.
> > > > > >
> > > > > > Assistance in using the relax prompt and scripting interface can be 
> > > > > > accessed by typing 'help' within
> > > > > > the prompt.
> > > > > >
> > > > > > Processor fabric:  Uni-processor.
> > > > > >
> > > > > > Best,
> > > > > > Andras
> > > > > >
> > > > > > ________________________________________
> > > > > > From: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] On 
> > > > > > Behalf Of Edward d'Auvergne [edward@xxxxxxxxxxxxx]
> > > > > > Sent: Friday, November 28, 2014 9:44 AM
> > > > > > To: Boeszoermenyi, Andras
> > > > > > Cc: relax-devel@xxxxxxx; Sébastien M
> > > > > > Subject: Re: [sr #3195] Fitting of saturation recovery experiment
> > > > > >
> > > > > > Hi,
> > > > > >
> > > > > > What do you see when you run:
> > > > > >
> > > > > > $ relax -i
> > > > > >
> > > > > > Are you using the latest relax trunk version?  Or the 3.3.3 version?
> > > > > > I only see this on versions 3.2.3 or earlier, in relax 3.3.0 and later
> > > > > > this works.
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > Edward
> > > > > >
> > > > > >
> > > > > >
> > > > > > On 28 November 2014 at 15:40, Boeszoermenyi, Andras
> > > > > > <Andras_Boeszoermenyi@xxxxxxxxxxxxxxx> wrote:
> > > > > > > That's exactly what I see.
> > > > > > >
> > > > > > > But you seem to be getting that error too, or am I mixing something 
> > > > > > > up now?
> > > > > > >
> > > > > > > Best,
> > > > > > > Andras
> > > > > > > ________________________________________
> > > > > > > From: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] On 
> > > > > > > Behalf Of Edward d'Auvergne [edward@xxxxxxxxxxxxx]
> > > > > > > Sent: Friday, November 28, 2014 9:34 AM
> > > > > > > To: Boeszoermenyi, Andras
> > > > > > > Cc: relax-devel@xxxxxxx; Sébastien M
> > > > > > > Subject: Re: [sr #3195] Fitting of saturation recovery experiment
> > > > > > >
> > > > > > > Hi Andras,
> > > > > > >
> > > > > > > That message is what happens when you execute the minimise.grid_search
> > > > > > > user function on an old relax version.  Could you check if you are
> > > > > > > running the latest:
> > > > > > >
> > > > > > > $ relax -i
> > > > > > >
> > > > > > > This is what I see with the last 3.1 relax release:
> > > > > > >
> > > > > > > """
> > > > > > >                                             relax 3.1.7
> > > > > > >
> > > > > > >                               Molecular dynamics by NMR data analysis
> > > > > > >
> > > > > > >                              Copyright (C) 2001-2006 Edward d'Auvergne
> > > > > > >                          Copyright (C) 2006-2014 the relax 
> > > > > > > development team
> > > > > > >
> > > > > > > This is free software which you are welcome to modify and redistribute
> > > > > > > under the conditions of the
> > > > > > > GNU General Public License (GPL).  This program, including all
> > > > > > > modules, is licensed under the GPL
> > > > > > > and comes with absolutely no warranty.  For details type 'GPL' within
> > > > > > > the relax prompt.
> > > > > > >
> > > > > > > Assistance in using the relax prompt and scripting interface can be
> > > > > > > accessed by typing 'help' within
> > > > > > > the prompt.
> > > > > > >
> > > > > > > Processor fabric:  Uni-processor.
> > > > > > >
> > > > > > > relax> minimise.grid_search()
> > > > > > > Traceback (most recent call last):
> > > > > > >   File "<console>", line 1, in <module>
> > > > > > > AttributeError: 'Uf_object' object has no attribute 'grid_search'
> > > > > > > """
> > > > > > >
> > > > > > > Regards,
> > > > > > >
> > > > > > > Edward
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On 28 November 2014 at 15:18, Boeszoermenyi, Andras
> > > > > > > <Andras_Boeszoermenyi@xxxxxxxxxxxxxxx> wrote:
> > > > > > > > Hi Edward,
> > > > > > > >
> > > > > > > > I upgraded everything to newest.
> > > > > > > >
> > > > > > > > I tried to updated the script too, but when I run it I get this 
> > > > > > > > error message:
> > > > > > > >
> > > > > > > > File "/sw/lib/relax-py27/multi/processor.py", line 494, in run
> > > > > > > >     self.callback.init_master(self)
> > > > > > > >   File "/sw/lib/relax-py27/multi/__init__.py", line 318, in 
> > > > > > > > default_init_master
> > > > > > > >     self.master.run()
> > > > > > > >   File "/sw/lib/relax-py27/relax.py", line 194, in run
> > > > > > > >     self.interpreter.run(self.script_file)
> > > > > > > >   File "/sw/lib/relax-py27/prompt/interpreter.py", line 275, in run
> > > > > > > >     return run_script(intro=self.__intro_string, local=locals(), 
> > > > > > > > script_file=script_file, show_script=self.__show_script, 
> > > > > > > > raise_relax_error=self.__raise_relax_error)
> > > > > > > >   File "/sw/lib/relax-py27/prompt/interpreter.py", line 578, in 
> > > > > > > > run_script
> > > > > > > >     return console.interact(intro, local, script_file, 
> > > > > > > > show_script=show_script, raise_relax_error=raise_relax_error)
> > > > > > > >   File "/sw/lib/relax-py27/prompt/interpreter.py", line 477, in 
> > > > > > > > interact_script
> > > > > > > >     exec_script(script_file, local)
> > > > > > > >   File "/sw/lib/relax-py27/prompt/interpreter.py", line 352, in 
> > > > > > > > exec_script
> > > > > > > >     runpy.run_module(module, globals)
> > > > > > > >   File "/sw/lib/python2.7/runpy.py", line 180, in run_module
> > > > > > > >     fname, loader, pkg_name)
> > > > > > > >   File "/sw/lib/python2.7/runpy.py", line 72, in _run_code
> > > > > > > >     exec code in run_globals
> > > > > > > >   File 
> > > > > > > > "/Users/andrasboeszoermenyi/relax-trunk/test_suite/shared_data/curve_fitting/saturation_recovery/relax_sym.py",
> > > > > > > >  line 106, in <module>
> > > > > > > >     minimise.grid_search(inc=11)
> > > > > > > > AttributeError: 'Uf_object' object has no attribute 'grid_search'
> > > > > > > >
> > > > > > > > Not sure if that could be related to my recent upgrade to Yosemite, 
> > > > > > > > but I think it shouldn't.
> > > > > > > >
> > > > > > > > I uploaded the project as:
> > > > > > > >
> > > > > > > > file #22996:  saturation_recovery.tar.gz
> > > > > > > >
> > > > > > > > Best,
> > > > > > > > Andras
> > > > > > > >
> > > > > > > > ________________________________________
> > > > > > > > From: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] On 
> > > > > > > > Behalf Of Edward d'Auvergne [edward@xxxxxxxxxxxxx]
> > > > > > > > Sent: Thursday, November 27, 2014 1:16 PM
> > > > > > > > To: Boeszoermenyi, Andras
> > > > > > > > Cc: relax-devel@xxxxxxx; Sébastien M
> > > > > > > > Subject: Re: [sr #3195] Fitting of saturation recovery experiment
> > > > > > > >
> > > > > > > > Hi Andras,
> > > > > > > >
> > > > > > > > I have now included your files in relax
> > > > > > > > (http://article.gmane.org/gmane.science.nmr.relax.scm/24542).  If you
> > > > > > > > have the trunk source code copy of relax and type:
> > > > > > > >
> > > > > > > > $ svn up
> > > > > > > >
> > > > > > > > You will see the files appear in the
> > > > > > > > test_suite/shared_data/curve_fitting/saturation_recovery directory.
> > > > > > > > If you could update your script for the latest relax version, I could
> > > > > > > > add it to the test_suite/system_tests/scripts/ directory.  This would
> > > > > > > > then be very simple to set up as a system test by duplicating and
> > > > > > > > modifying this test:
> > > > > > > >
> > > > > > > > http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_fit-pysrc.html#Relax_fit.test_zooming_grid_search
> > > > > > > >
> > > > > > > > Cheers,
> > > > > > > >
> > > > > > > > Edward
> > > > > > > >
> > > > > > > >
> > > > > > > > On 27 November 2014 at 19:06, Edward d'Auvergne 
> > > > > > > > <edward@xxxxxxxxxxxxx> wrote:
> > > > > > > > > Hi Andras,
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > > ok I uploaded a tar file with synthetic peaks for one spin system:
> > > > > > > > > >
> > > > > > > > > > file #22989
> > > > > > > > >
> > > > > > > > > Cheers!  The permanent link to the file is
> > > > > > > > > http://gna.org/task/download.php?file_id=22989, and this is attached
> > > > > > > > > to the task #7415 (http://gna.org/task/?7415).
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > > The saturation recovery formula is:
> > > > > > > > > >
> > > > > > > > > >  I0*(1 - exp(?R1*t))
> > > > > > > > > >
> > > > > > > > > > The parameters I used were
> > > > > > > > > >
> > > > > > > > > > I0 = 1000000000000000.00
> > > > > > > > > >
> > > > > > > > > > and
> > > > > > > > > >
> > > > > > > > > > R1 = 0.5
> > > > > > > > >
> > > > > > > > > I'm wondering if this equation is correct.  Should this not be:
> > > > > > > > >
> > > > > > > > > I(t) = I_inf*(1 - exp(?R1*t))
> > > > > > > > >
> > > > > > > > > Is the magnitisation not returning to the steady-state of I_inf?  I
> > > > > > > > > guess that in this experiment I0 == I_inf.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > > Obviously, the same numbers also work for the inversion recovery 
> > > > > > > > > > experiment:
> > > > > > > > > >
> > > > > > > > > > I(t) = I? ? I0*exp(?R1*t)
> > > > > > > > > >
> > > > > > > > > > with I? set to 1000000000000000.00 as well. Not sure how much that 
> > > > > > > > > > helps though.
> > > > > > > > >
> > > > > > > > > If I0 is set to something less than I_inf, this would give different
> > > > > > > > > I(t) values.  Such a data set could be used to implement the 
> > > > > > > > > inversion
> > > > > > > > > recovery experiment.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > > If "inv" is not implemented, then that would explain the weird 
> > > > > > > > > > results :)
> > > > > > > > >
> > > > > > > > > More of a warning is probably required.  Or a synthetic data set,
> > > > > > > > > relax script, and system test created, and then this equation 
> > > > > > > > > finally
> > > > > > > > > implemented.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > > Unfortunately, I have no primary reference for the saturation 
> > > > > > > > > > recovery experiment either.
> > > > > > > > >
> > > > > > > > > It's a pity.  The ancient primary references for all these basic and
> > > > > > > > > old experiment types would be great for adding to the relax manual 
> > > > > > > > > and
> > > > > > > > > user function documentation.  I can see that lots of people discuss
> > > > > > > > > this older method, but I also don't see any references.
> > > > > > > > >
> > > > > > > > > I was wondering if you were able to update to the latest version of
> > > > > > > > > relax (3.3.3 at http://www.nmr-relax.com/download.html#Mac_OS_X), or
> > > > > > > > > even better to use the relax trunk source code
> > > > > > > > > (http://thread.gmane.org/gmane.science.nmr.relax.devel/3693/focus=7348).
> > > > > > > > > Could you try to update the scripts to run with these versions?  The
> > > > > > > > > newest relax versions will tell you how the user functions have been
> > > > > > > > > renamed.
> > > > > > > > >
> > > > > > > > > Cheers,
> > > > > > > > >
> > > > > > > > > Edward