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 #22989Cheers! 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 = 0.5I'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