Hi Mengjun,
If you have already downloaded the relax trunk source code, you can
update this to the latest version with the command:
$ svn up
You need to be in the base relax directory. Then to run the
sample_scripts/relax_disp/cpmg_analysis.py script, you need to be in
the
Oh, the answer to your question is that you should not see such a
problem. It should be solved.
Regards,
Edward
On 2 May 2014 11:08, Edward d'Auvergne edw...@nmr-relax.com wrote:
Hi Mengjun,
If you have already downloaded the relax trunk source code, you can
update this to the latest
Hi,
You should also have a look at the sample_scripts/README file I just
added. And Troels modified the relaxation dispersion sample scripts
so that you can run them from anywhere. To get these changes, run
'svn up' if you already have the source code.
Regards,
Edward
On 2 May 2014 20:04,
Hi Edward,
Thank you so much for your suggestions. It is very helpful.
Best regards,
Mengjun
Quoting Edward d'Auvergne edw...@nmr-relax.com:
Oh, the answer to your question is that you should not see such a
problem. It should be solved.
Regards,
Edward
On 2 May 2014 11:08, Edward
Hi Edward,
Thank you very much. I will try it as you suggested. I understand that
the new version of Relax will solve such problem ? Thank you.
Best regards,
Mengjun
Quoting Edward d'Auvergne edw...@nmr-relax.com:
Hi Mengjun,
To test this, if you have subversion installed on your
Hi Edward,
Thank you very much. Will the problem of bug be solved ? so I will be
able to run cpmg_analysis.py on my computer?
Best regards,
Mengjun
Quoting Edward d'Auvergne edw...@nmr-relax.com:
Hi,
You're right! After looking at that for a while, I can see that that
feature is not
Hi Mengjun,
To test this, if you have subversion installed on your computer you
can download the most recent relax code and test it yourself. The
steps required are explained at
http://www.nmr-relax.com/download.html#Source_code_repository and at
http://www.nmr-relax.com/windows_devel.html#svn.
Hi,
You're right! After looking at that for a while, I can see that that
feature is not working any more! It used to be that the --log and
--tee options worked with all the other relax options, but somehow
they got mixed up (you can see the incorrect order in the run() method
of the relax.py
Hi Edward,
I have copy the entire relax-3.1.7 directory to C:\, and run
cpmg_analysis.py, error is still there, please see the debug log file:
relax 3.1.7
Molecular dynamics by NMR data analysis
Copyright (C)
Hi Mengjun,
Try modifying your path so there is a '\' after the 'C:' part.
Regards,
Edward
On 24 April 2014 10:56, mengjun@mailbox.tu-berlin.de wrote:
Hi Edward,
I have copy the entire relax-3.1.7 directory to C:\, and run
cpmg_analysis.py, error is still there, please see the debug
Hi Mengjun,
I have tried to replicate everything you have done, placing relax
3.1.7 into C:\Program files\Relax-3.1.7, copying the sample script,
and modifying the data path to be 'C:\Program
files\Relax-3.1.7\\test_suite\
shared_data\dispersion\Hansen', but I just cannot reproduce this issue.
Hi Edward,
I have tried the 'relax -i --tee log' command, but it does not create
log file on my computer, I just copy the output from cmd window using
editor mode:
relax 3.1.7
Molecular dynamics by NMR data analysis
Hi,
If the 'relax -i --tee log' command does not produce a 'log' file on
your computer, then that indicates where the problem is. There are
only two cases where this file cannot be produced:
- The 'log' file already exists. The old file would therefore have
to be deleted, or run 'relax -i
Hi Edward,
When I run relax -i --tee log, I rename log to log123 or loglog, which
is new name, it should not be problem. For the permisions for the
directory, I can get the log file when I run other script, for
example, I have run dauvergne_protocol.py for the full model free
analysis on
Hi Mengjun,
When you run 'relax -i --tee log', there is no script being run. Does
this still not produce the 'log' file from the directory you ran it
from? I'm deliberately ignoring the 'cpmg_analysis.py' script right
now to try to understand and pinpoint where on earth this strange
behaviour
Hi Edward,
I tried the 'relax -i --tee log' command, C:\relax-3.1.7\relax -i
--tee log6, I entered the command line 'relax -i --tee log' under cmd,
following output show up in the cmd window (I copied the output in cmd
window using editor mode), but no log6 file is created in the
Hi,
Try the following then, in the Command Prompt window:
C:\relax-3.1.7 dir test
I.e. run 'dir test'. If you see the text Access is denied, then
that means that you do not have permission to create files in that
directory. Is this what you see?
Regards,
Edward
On 24 April 2014 18:13,
Hi Edward,
I tried the C:\relax-3.1.7 dir test, I did not see the text
Access is denied,
please see the following output:
Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.
C:\Users\xmjcd..
C:\Users\cd..
'\cd..' is not recognized as an
Hi,
Do you then see the file C:\relax-3.1.7\test? This must now exist.
Regards,
Edward
On 24 April 2014 18:26, mengjun@mailbox.tu-berlin.de wrote:
Hi Edward,
I tried the C:\relax-3.1.7 dir test, I did not see the text Access is
denied,
please see the following output:
Hi Edward,
Yes, I see the file C:\relax-3.1.7\test, please see the following
information of the test file.
Volume in drive C has no label.
Volume Serial Number is B035-71CF
Directory of C:\relax-3.1.7
04/24/2014 06:21 PMDIR .
04/24/2014 06:21 PMDIR ..
Hi,
Could you then run, in cmd:
C:\relax-3.1.7 relax --tee log_new
...
relax print Hello
relax quit
C:\relax-3.1.7
And then see if you have the 'log_new' file in that directory. Also run:
C:\relax-3.1.7 relax --info --log log_info
And search for the file 'log_info'.
Regards,
Edward
On
Hi Edward,
I have ran in cmd:
C:\relax-3.1.7 relax --tee log_new
...
relax print Hello
relax quit
C:\relax-3.1.7
I can find the log_new file, please following:
relax 3.1.7
Molecular dynamics by NMR data analysis
URL:
http://gna.org/bugs/?21959
Summary: cpmg_analysis
Project: relax
Submitted by: None
Submitted on: Wed 23 Apr 2014 09:43:15 AM UTC
Category: relax sample scripts
Specific analysis category: None
Update of bug #21959 (project relax):
Status:None = Invalid
Assigned to:None = bugman
Open/Closed:Open = Closed
Hi Edward,
Thank you so much for the detailed information about setting data
path, as you suggested I have set data path in cpmg_analysis.py to:
DATA_PATH = 'C:\Program
files\Relax-3.1.7\\test_suite\shared_data\dispersion\Hansen' or
DATA_PATH = 'C:\Program
Hi,
Could you list the entire contents of the '500_MHz' folder? I must
absolutely contain that file! You can do this by running dir log
and opening the 'log' text file. I have done this on a virtual
machine and see:
Directory:
Hi Mengjun,
I also just checked the contents of the officially released relax
3.1.7 MS Windows distribution zip file. The reference.in_sparky file
is in that directory. Note that 'fake_sequence.in' is not in that
directory - it is in the parent
test_suite/shared_data/dispersion/Hansen/
Hi Edward,
Thank you. I have made the log file for dir, it seems it is same to yours:
Directory of C:\Program
Files\relax-3.1.7\test_suite\shared_data\dispersion\Hansen\500_MHz
04/23/2014 03:24 PMDIR .
04/23/2014 03:24 PMDIR ..
03/17/2014 03:11 PM
Hi,
There is no '500_reference.in' file. This is not the name of the file
but is the spectrum ID string used in relax to handle spectral data
from different spectra. Therefore all the data read out of the
'reference.in_sparky' file will be associated with the ID
'500_reference.in'. So if you
Hi Edward,
Thank you. Should I run debug command in this way:
C:\program files\relax-3.1.7\relax --debug --tee log_debug cpmg_analysis.py,?
Best regards,
Mengjun
Quoting Edward d'Auvergne edw...@nmr-relax.com:
Hi Mengjun,
Could you also run the script in debugging mode - with the
Hi,
That should work. It will record the source of the error.
Cheers,
Edward
On 23 April 2014 15:56, mengjun@mailbox.tu-berlin.de wrote:
Hi Edward,
Thank you. Should I run debug command in this way:
C:\program files\relax-3.1.7\relax --debug --tee log_debug
cpmg_analysis.py,?
Hi Edward,
I have set data path in cpmg_analysis.py to:
DATA_PATH = 'C:\Program
files\Relax-3.1.7\test_suite\shared_data\dispersion\Hansen'
and run the cpmg_analysis.py under cmd,C:\program
files\relax-3.1.7\relax --debug --tee log_debug cpmg_analysis.py,
please see following output of
Hi Mengjun,
Looking at which user functions have been run, I can now see that the
following one is missing:
sequence.read('fake_sequence.in', dir=DATA_PATH, res_num_col=1, res_name_col=2)
From the log files attached to https://gna.org/bugs/?21959, I can see
that this line has been deleted from
Hi Edward,
I have downloaded relax-3.1.7 again, and copy the new
cpmg_analysis.py, which include # Load the sequence.
sequence.read('fake_sequence.in', dir=DATA_PATH, res_num_col=1,
res_name_col=2), and run again, C:\program files\relax-3.1.7\relax
--debug --tee log_debug cpmg_analysis.py,
Hi,
One failure source in Python with paths is sometimes if there is a
space in a file or directory name. Is it possible to copy the entire
relax-3.1.7 directory to C:\ so it is not in 'Program files', and then
run this again? I'll look into the relax lib\io.py file tomorrow to
see if that
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