Hi, This error is because you have not recorded duplicate spectra. In this case you will need to measure the RMSD of the baseplane noise (Tom Goddard added that feature for me into Sparky in the extension menu, if you are using sparky). Unfortunately the GUI cannot handle this concept yet. However you could use the scripting interface as this is fully supported. All of this is described in the spectrum.error_analysis() user function documentation (try typing 'help(spectrum.error_analysis)' at the relax prompt).
As for the spin ID string notation, from the documentation it is described as: """ Identification string documentation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The identification string is composed of three components: the molecule id token beginning with the '#' character, the residue id token beginning with the ':' character, and the atom or spin system id token beginning with the '@' character. Each token can be composed of multiple elements separated by the ',' character and each individual element can either be a number (which must be an integer, in string format), a name, or a range of numbers separated by the '-' character. Negative numbers are supported. The full id string specification is '#<mol_name> :<res_id>[, <res_id>[, <res_id>, ...]] @<atom_id>[, <atom_id>[, <atom_id>, ...]]', where the token elements are '<mol_name>', the name of the molecule, '<res_id>', the residue identifier which can be a number, name, or range of numbers, '<atom_id>', the atom or spin system identifier which can be a number, name, or range of numbers. If one of the tokens is left out then all elements will be assumed to match. For example if the string does not contain the '#' character then all molecules will match the string. Regular expression can be used to select spins. For example the string '@H*' will select the protons 'H', 'H2', 'H98'. """ This means that '#refinadas_mol1:5&:VAL@49&@N' refers to the molecule refinadas_mol1, residue Val 5, atom 49 N. Regards, Edward On 4 July 2011 15:25, Aldino <[email protected]> wrote: > Hi, > > so, it now reads the lists OK. > Nevertheless I get the following when calculating either R1 or R2: > > .... > File > "/home/aldino/Documents/Software/relax-1.3/gui/analyses/auto_rx_base.py", > line 290, in execute_thread > Relax_fit(file_root=self.filename, > pipe_name='rx'+'_'+str(time.asctime(time.localtime())), > seq_args=data.seq_args, results_directory=data.save_dir, > file_names=data.file_names, relax_times=data.relax_times, > int_method=data.int_method, mc_num=data.mc_num, > pdb_file=data.structure_file, unresolved=data.unresolved, view_plots = > False, heteronuc=data.heteronuc, proton=data.proton, > load_spin_ids=data.load_spin_ids, inc=data.inc) > File > "/home/aldino/Documents/Software/relax-1.3/auto_analyses/relax_fit.py", line > 106, in __init__ > self.run() > File > "/home/aldino/Documents/Software/relax-1.3/auto_analyses/relax_fit.py", line > 142, in run > self.interpreter.spectrum.error_analysis() > File "/home/aldino/Documents/Software/relax-1.3/prompt/spectrum.py", line > 221, in error_analysis > spectrum.error_analysis() > File "/home/aldino/Documents/Software/relax-1.3/generic_fns/spectrum.py", > line 632, in error_analysis > __errors_height_no_repl() > File "/home/aldino/Documents/Software/relax-1.3/generic_fns/spectrum.py", > line 336, in __errors_height_no_repl > raise RelaxError("The RMSD of the base plane noise for spin '%s' has not > been set." % spin_id) > relax_errors.RelaxError: RelaxError: The RMSD of the base plane noise for > spin '#refinadas_mol1:5&:VAL@49&@N' has not been set. > > What does the last line (in bold) means? I don't have any VAL49..... > > > Cheers, > Aldino > > > -----Mensagem Original----- From: Edward d'Auvergne > Sent: Monday, July 04, 2011 12:43 PM > To: Aldino > Cc: [email protected] > Subject: Re: R1 and R2 calculation error > > Hi, > > Don't worry about most of these issues, remember that this code that > is in development and the released version will be different. The > Gtk-WARNING issues are only part of the GUI coding and don't affect > its usage. For the "Single delay cycle time" and "Nº of cycles", > these don't have tooltips yet to describe what they are. It is > essentially the time for one cycle or one unit of the delay time in > the R1 and R2 pulse sequence, and the number of times this is > repeated. You can skip this though and put the times in directly. > > The major problem you are experiencing is that your data is not being > read out of the peak lists. That is because the proton name is 'HN'. > If you go to the global settings window, you will see that the proton > name defaults to 'H'. If you change this, the data should be read and > everything should hopefully then work. > > Regards, > > Edward > > > > > > On 4 July 2011 13:21, Aldino <[email protected]> wrote: >> >> Dear Edward, >> indeed now it works (at least I don´t get that error...). >> Unfortunately I have new problems and questions.... >> >> So, first of all, in the R1 and R2 relaxation windows what does it mean >> the >> "Single delay cycle time" and "Nº of cycles"? >> >> Second, when I open the GUI I get (I don't know what this means): >> >> (python:3321): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to >> allocate widget with width -5 and height 19 >> >> (python:3321): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to >> allocate widget with width -5 and height 19 >> >> (python:3321): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to >> allocate widget with width -5 and height 19 >> >> (python:3321): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to >> allocate widget with width -5 and height 19 >> >> (python:3321): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to >> allocate widget with width -5 and height 19 >> >> (python:3321): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to >> allocate widget with width -5 and height 19 >> >> >> >> Now, when I run the R1 calculations it seems that it does not recognize >> the >> lists... At some point I get: >> >> .... >> >> Number of header lines found: 1 >> RelaxWarning: Proton and heteronucleus names do not match, skipping the >> data >> ['Assignment', 'w1', 'w2', 'Volume']. >> RelaxWarning: Proton and heteronucleus names do not match, skipping the >> data >> ['V5N-HN', '119.415', '7.656', '23500.6']. >> .... >> >> Of course that in the end I don't have any R1 values... >> Is there something that I have to change in the lists? They are the same I >> sent for the bug report (but with all the data).... >> >> >> Finally, when I run the R2 calculations apparently it reads the lists >> (that >> were created exactly as the T1 lists) but then I get: >> >> ... >> relax> spectrum.error_analysis() >> Intensity measure: Peak heights. >> Replicated spectra: No. >> Unhandled exception in thread started by >> Traceback (most recent call last): >> File >> "/home/aldino/Documents/Software/relax-1.3/gui/analyses/auto_rx_base.py", >> line 290, in execute_thread >> Relax_fit(file_root=self.filename, >> pipe_name='rx'+'_'+str(time.asctime(time.localtime())), >> seq_args=data.seq_args, results_directory=data.save_dir, >> file_names=data.file_names, relax_times=data.relax_times, >> int_method=data.int_method, mc_num=data.mc_num, >> pdb_file=data.structure_file, unresolved=data.unresolved, view_plots = >> False, heteronuc=data.heteronuc, proton=data.proton, >> load_spin_ids=data.load_spin_ids, inc=data.inc) >> File >> "/home/aldino/Documents/Software/relax-1.3/auto_analyses/relax_fit.py", >> line >> 106, in __init__ >> self.run() >> File >> "/home/aldino/Documents/Software/relax-1.3/auto_analyses/relax_fit.py", >> line >> 142, in run >> self.interpreter.spectrum.error_analysis() >> File "/home/aldino/Documents/Software/relax-1.3/prompt/spectrum.py", line >> 221, in error_analysis >> spectrum.error_analysis() >> File "/home/aldino/Documents/Software/relax-1.3/generic_fns/spectrum.py", >> line 632, in error_analysis >> __errors_height_no_repl() >> File "/home/aldino/Documents/Software/relax-1.3/generic_fns/spectrum.py", >> line 336, in __errors_height_no_repl >> raise RelaxError("The RMSD of the base plane noise for spin '%s' has not >> been set." % spin_id) >> relax_errors.RelaxError: RelaxError: The RMSD of the base plane noise for >> spin '#refinadas_mol1:5&:VAL@49&@N' has not been set. >> >> >> And in the end I don't get any values.... >> >> Sorry for all the questions and doubts! >> >> Sincerely, >> Aldino >> >> >> >> >> -----Mensagem Original----- From: Aldino >> Sent: Friday, July 01, 2011 2:29 PM >> To: Edward d'Auvergne >> Cc: [email protected] >> Subject: Re: R1 and R2 calculation error >> >> Dear Edward, >> >> First of all, thank you very much for your help. >> You can use the truncated data (always glad to help). >> I will try to use the fixed code and let you know how it went. >> >> Sincerely, >> Aldino >> >> >> -----Mensagem Original----- From: Edward d'Auvergne >> Sent: Friday, July 01, 2011 12:50 PM >> To: Aldino >> Cc: [email protected] >> Subject: Re: R1 and R2 calculation error >> >> Hi, >> >> I have now fixed the bug in the main 1.3 line. The problem was that >> the variable 'ds.relax_gui.sequencefile' did not exist, it had been >> renamed. So I have used your data and successfully calculated the R2 >> values. I was wondering if it would be ok to add your truncated data >> to the relax test suite so that I could be sure that such a bug never >> returns? It would be much appreciated. >> >> One issue still is that the GUI is not very flexible and you cannot >> currently specify which columns of your sequence file correspond to >> residue names, residue numbers, spin numbers, etc. It is hardcoded to >> assume that a residue is in the first column :S The prompt/scripting >> based interface does not have this problem and you can have your >> sequence data in any format. This is one of the reasons why I am >> currently rewriting the entire GUI - to eliminate such undocumented >> inflexibilities. For the new design you will have to wait. >> Unfortunately it will also take me a while before I can release a new >> version of relax. However if you would like to use the fixed code, >> you could follow the instructions at >> http://www.nmr-relax.com/download.html#Source_code_repository. Note >> for the R1 and R2, you will need to have the python development >> libraries installed and the scons program (as well as a C compiler). >> See the instructions at >> http://www.nmr-relax.com/download.html#Source_code_release. If this >> is not possible and you cannot wait, you could try the relax_fit.py >> sample script (in the sample_script directory) and run this from the >> command line. >> >> Regards, >> >> Edward >> >> >> >> On 27 June 2011 12:44, Aldino <[email protected]> wrote: >>> >>> Dear Edward, >>> >>> I ran relax -g --debug and I got the following: >>> >>> >>> File "/home/aldino/Software/relax-1.3.10/gui/analyses/auto_rx_base.py", >>> line 438, in execute >>> self.execute_thread('dummy') >>> File "/home/aldino/Software/relax-1.3.10/gui/analyses/auto_rx_base.py", >>> line 463, in execute_thread >>> data, complete, missing = self.assemble_data() >>> File "/home/aldino/Software/relax-1.3.10/gui/analyses/auto_rx_base.py", >>> line 288, in assemble_data >>> data.seq_args = [ds.relax_gui.sequencefile, None, None, 1, None, None, >>> None, None] >>> AttributeError: 'Gui' object has no attribute 'sequencefile' >>> >>> It seems that it has some problem with the sequence.... >>> >>> the file I am using is of the type (*.seq): >>> >>> MET 1 >>> ALA 2 >>> SER 3 >>> ALA 4 >>> ... >>> >>> and it works for the NOE calculation... >>> In the meanwile I am writing the bug report. >>> >>> Cheers, >>> Aldino >>> >>> >>> >>> >>> -----Mensagem Original----- From: Edward d'Auvergne >>> Sent: Monday, June 27, 2011 10:08 AM >>> To: Aldino >>> Cc: [email protected] >>> Subject: Re: R1 and R2 calculation error >>> >>> Hi, >>> >>> Thank you for the information. I've been looking into this problem, >>> but it is hard to diagnose. There has been a bug triggered somewhere >>> in the setup of the data (I think) but as this is running in a thread, >>> the relax error message is not being caught and reported. That is the >>> meaning of "Unhandled exception in thread". So the real cause is >>> lost. There is a way of bypassing this by using the debug flag. I.e. >>> running relax as: >>> >>> $ relax -g --debug >>> >>> This will cause the real source of the error to be printed in the >>> terminal/shell in which you launched relax. It would be very useful >>> if you were to report this in a bug report though, including a tiny, >>> randomised data set which still triggers the bug >>> (https://gna.org/bugs/?func=additem&group=relax). Having the data >>> will allow me to very quickly reproduce the bug and hopefully have a >>> fix within ~5 min. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 27 June 2011 10:39, Aldino <[email protected]> wrote: >>>> >>>> Dear Edward, >>>> >>>> once again, thank you for your reply. This time I´ll make sure the >>>> message >>>> goes to the mailing list. >>>> So, here it goes: >>>> >>>> I am using the latest Relax version (3.1.10) >>>> >>>> Below I send the relax info (also in attach): >>>> >>>> relax 1.3.10 >>>> >>>> Molecular dynamics by NMR data analysis >>>> >>>> Copyright (C) 2001-2006 Edward d'Auvergne >>>> Copyright (C) 2006-2011 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. >>>> >>>> Hardware information: >>>> Machine: i686 >>>> Processor: i686 >>>> >>>> System information: >>>> System: Linux >>>> Release: 2.6.38-8-generic >>>> Version: #42-Ubuntu SMP Mon Apr 11 03:31:50 UTC 2011 >>>> GNU/Linux version: Ubuntu 11.04 natty >>>> Distribution: Ubuntu 11.04 natty >>>> Full platform string: >>>> Linux-2.6.38-8-generic-i686-with-Ubuntu-11.04-natty >>>> >>>> Software information: >>>> Architecture: 32bit ELF >>>> Python version: 2.7.1+ >>>> Python branch: tags/r271 >>>> Python build: r271:86832, Apr 11 2011 18:05:24 >>>> Python compiler: GCC 4.5.2 >>>> Python implementation: CPython >>>> Python revision: 86832 >>>> Numpy version: 1.5.1 >>>> Libc version: glibc 2.4 >>>> >>>> Python packages (most are optional): >>>> >>>> Package Installed Version Path >>>> minfx True Unknown >>>> /home/aldino/Software/relax-1.3.10/minfx >>>> bmrblib False >>>> numpy True 1.5.1 >>>> /usr/lib/pymodules/python2.7/numpy >>>> ScientificPython True 2.8 >>>> /usr/lib/python2.7/dist-packages/Scientific >>>> wxPython True >>>> mpi4py False >>>> epydoc False >>>> optparse True 1.5.3 >>>> /usr/lib/python2.7/optparse.pyc >>>> Numeric False >>>> readline True >>>> /usr/lib/python2.7/lib-dynload/readline.so >>>> profile True >>>> /usr/lib/python2.7/profile.pyc >>>> bz2 True >>>> /usr/lib/python2.7/lib-dynload/bz2.so >>>> gzip True >>>> /usr/lib/python2.7/gzip.pyc >>>> os.devnull True >>>> /usr/lib/python2.7/os.pyc >>>> >>>> Compiled relax C modules: >>>> Relaxation curve fitting: True >>>> >>>> >>>> In the mean wile I will try to submit a bug report for this. >>>> >>>> Thanks, >>>> Aldino >>>> >>>> -----Mensagem Original----- From: Edward d'Auvergne >>>> Sent: Wednesday, June 22, 2011 3:35 PM >>>> To: Aldino >>>> Cc: [email protected] >>>> Subject: Re: R1 and R2 calculation error >>>> >>>> Dear Aldino, >>>> >>>> Welcome to the relax mailing lists. The problem you are seeing could >>>> possibly be related to an older version of relax. Which version are >>>> you using? Could you copy and paste the output of: >>>> >>>> $ relax --info >>>> >>>> If you are using version 1.3.9 or earlier, I would recommend trying >>>> out 1.3.10 and see if the problem is solved. If you are using version >>>> 1.3.10, you have encountered a new bug. If so, would you be able to >>>> submit a bug report for this? See >>>> https://gna.org/bugs/?func=additem&group=relax. I would recommend >>>> including a minimal data set (only data for one or two spins, >>>> randomised if you would like to keep it private) and instructions for >>>> how to trigger the bug. >>>> >>>> Cheers, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 21 June 2011 18:05, Aldino <[email protected]> wrote: >>>>> >>>>> Hi! >>>>> >>>>> I have just started using RelaxGUI and I’m having some problems when >>>>> trying >>>>> to calculate R1 and R2. >>>>> >>>>> For the steady-state NOE everything is alright but when I start the R1 >>>>> calculation I get: >>>>> >>>>> >>>>> >>>>> “Starting R1 calculation >>>>> >>>>> Unhandled exception in thread started by <bound method >>>>> Auto_r1.execute_thread of <gui.analyses.auto_r1.Auto_r1 instance at >>>>> 0xa47556c>>” >>>>> >>>>> >>>>> >>>>> The same thing when trying to calculate R2... >>>>> >>>>> >>>>> >>>>> “Starting R2 calculation >>>>> >>>>> Unhandled exception in thread started by <bound method >>>>> Auto_r2.execute_thread of <gui.analyses.auto_r2.Auto_r2 instance at >>>>> 0xa46f4cc>>” >>>>> >>>>> >>>>> >>>>> Please help... >>>>> Thanks, >>>>> Aldino >>>>> >>>>> >>>>> >>>>> ______________________________________________ >>>>> Aldino Viegas, PhD Student >>>>> Dep. Química, REQUIMTE >>>>> Faculdade de Ciências e Tecnologia >>>>> Universidade Nova de Lisboa >>>>> 2829-516 Caparica, Portugal >>>>> >>>>> Tlf. +351 212948300 >>>>> Ext. 10900 Lab. 106-A >>>>> [email protected] >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> >>>> >>> >>> >> >> >> _______________________________________________ >> 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 >> > > _______________________________________________ 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
