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 <[EMAIL PROTECTED]>: > 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 > <[EMAIL PROTECTED]> wrote: >> 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 >> > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
