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: relax-users@xxxxxxx
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: relax-users@xxxxxxx
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 <aldinoviegas@xxxxxxxxxxxxx> 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: relax-users@xxxxxxx
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 <aldinoviegas@xxxxxxxxxxxxx> 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: relax-users@xxxxxxx
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 <aldinoviegas@xxxxxxxxxxxxx> 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
aldinoviegas@xxxxxxxxxxxxx
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-users mailing list
relax-users@xxxxxxx
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
relax-users@xxxxxxx
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
Re: R1 and R2 calculation error