Hi
I am trying to run relax with the graphical user interface, but I get the
following error when I typ ³relax g²:
RelaxError: no such option: -g
Can someone explain me what is wrong, why it doesn¹t work and have a
solution?
Many thanks, Nico
Dr. Ir. Nico van Nuland, PhD
VIB group leader Biom
I had sent the error report as a text file for the o/p of
relax --test-suite on x86_64-linux on centOS5.
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Dear Nico,
Welcome to the relax mailing lists. The problem is likely to be that
you are using an old version of relax. You can see when you start
relax without the '-g' option, the version must be greater than 1.3.9
for the graphical interface. If this is not the case, have a look at
http://www
Hi Edward
Thanks for your fast reply!
I am working on a Mac, and used " fink install relax-py25".
I guess with that I installed the last version doing this, or not?
When I type "relax --info" I get a similar error: RelaxError: no such option
All best, Nico
PS I am able to run relax, for instanc
Hi,
Not a problem. Unfortunately the relax version in fink is quite old.
That version is 1.3.4
(http://pdb.finkproject.org/pdb/browse.php?name=relax). You will
therefore have to use the source code releases
(http://www.nmr-relax.com/download.html#Source_code_release). These
will require a bit m
Hi Nico,
If, when you try to install relax from the source code repository on
your Mac, you encounter problems, please feel free to ask for help.
I have successfully installed relax this way on my Mac !
Best of luck,
Séb :)
On 11-06-15 5:27 PM, Edward d'Auvergne wrote:
Hi,
Not a proble
On Wed, Jun 15, 2011 at 05:27:04PM +0200, Edward d'Auvergne wrote:
> Hi,
>
> Not a problem. Unfortunately the relax version in fink is quite old.
> That version is 1.3.4
> (http://pdb.finkproject.org/pdb/browse.php?name=relax). You will
> therefore have to use the source code releases
> (http://
Hi Jack,
Thank you for your work with fink! Maybe Seb can help you with
testing. If there is anything which could be added to the sconstruct
scripts, please say and I can do that. If it can be worked out how to
handle this, via darwin version checking or another method, it would
be good to inte
Hi Jack,
Of course, if this can be of any help, I could test the fink versions of
relax on my own system...
Cheers,
Séb :)
On 11-06-15 5:49 PM, Edward d'Auvergne wrote:
Hi Jack,
Thank you for your work with fink! Maybe Seb can help you with
testing. If there is anything which could be
Hi Venkat,
I have seen the log file attached to your bug report
(https://gna.org/bugs/?19987). There seems to be two separate issues
here. The first is the two failures in the system tests. As you can
probably see, this is for Art Palmer's Modelfree4 program. From the
lower precision of the ch
Hi,
Do you have the wx demos? You can download them from
http://downloads.sourceforge.net/wxpython/wxPython-demo-2.8.12.1.tar.bz2
and run these directly. The results of the following tests are
important:
$ /programs/x86_64-linux/python/2.7.2/bin/python run.py GenericButtons.py
$ /programs/x86_6
Hi ,
Here is how wx-python was installed.
./configure --prefix=/programs/x86_64-linux/wxpython/2.8.12.1
--enable-unicode --with-gtk --with-gnomeprint --with-opengl
--with-libjpeg=builtin --with-libpng=builtin --with-libtiff=builtin
--with-zlib=builtin --enable-optimize --enable-debug_flag
--enabl
Hi Edward,
Here is the o/p of the wx tests.
$ which python
/programs/x86_64-linux/python/2.7.2/bin/python
sbtest@vm-11 [centos-5-x86_64] ~/test/relax/wxtest/demo
$ python run.py Ge
GenericButtons.py GenericDirCtrl.py GetMouseState.py
sbtest@vm-11 [centos-5-x86_64] ~/test/relax/wxtest/demo
$ p
Hi,
Those are very strange errors! It might be an indication that the
wxPython compilation failed. Does the version.py file that came with
the wxPython demos match the wxPython version you have installed? I
would suggest trying the 2.9 wxPython versions, or having a close look
at the compilatio
Hi Edward,
To make sure wx_python has issues I tried the following:
I tried the earlier version of relax 1.3.16 via ssh and that seg faults.
But relax version 1.3.16 works when use RDP and try it with the same
wx_python.
venkat
On Thu, Aug 9, 2012 at 9:03 PM, Edward d'Auvergne wrote:
> Hi,
>
n and test that instead. As the internal tests of the
wxPython demos fail, then there will be no way to ever make the
wxPython execute the relax GUI. These tests must, without question,
pass otherwise there is no point even trying the relax GUI as the GUI
will never work. If you can compile the
stead. As the internal tests of the
> wxPython demos fail, then there will be no way to ever make the
> wxPython execute the relax GUI. These tests must, without question,
> pass otherwise there is no point even trying the relax GUI as the GUI
> will never work. If you can compile the lates
100% sure that the
>> problem is, however, the wxPython installation. Please try to compile
>> the 2.9 version and test that instead. As the internal tests of the
>> wxPython demos fail, then there will be no way to ever make the
>> wxPython execute the relax GUI. These tests
Hi Edward,
> I was wondering if you'd had success with the newer wxPython versions?
We haven't tried it yet.
> Are the demo scripts running?
Yes, the demo scripts all work fine with our existing wxPython
installation. relax version 1.3.16 also works fine with the existing
installation, so it's
Hi Ben,
My suggestion to switch to the newer wxPython version was because of
Venkat's message archived at:
http://article.gmane.org/gmane.science.nmr.relax.user/1251
As he reported that the execution of the GenericButtons.py demo script with
$ python run.py GenericButtons.py
failed, and this i
Hi Venkat,
I've been doing a number of tests, but unfortunately I cannot
reproduce this problem at all. I can ssh into a machine 500 km away
and run the relax GUI on my laptop without problem. I can also ssh
between a number of different machines and run the GUI. Could you
test if the GUI
umber of tests, but unfortunately I cannot
> reproduce this problem at all. I can ssh into a machine 500 km away
> and run the relax GUI on my laptop without problem. I can also ssh
> between a number of different machines and run the GUI. Could you
> test if the GUI will run directl
from the command prompt with:
$ relax --test-suite
It will be interesting to see if you see a segfault after the system
and unit tests, just when the GUI tests start. Could you also run the
individual test categories with:
$ relax --system-tests
$ relax --unit-tests
$ relax --gui-tests
The firs
-suite
>
> It will be interesting to see if you see a segfault after the system
> and unit tests, just when the GUI tests start. Could you also run the
> individual test categories with:
>
> $ relax --system-tests
> $ relax --unit-tests
> $ relax --gui-tests
>
> The fi
Hi,
I have relax running on my Ubuntu 12.04 laptop, and am running into a problem
with the GUI. When trying to set up spin systems, the spin loading page is
unable to be resized, and the buttons at the bottom are not visible, and thus
not clickable.
I have tried playing with the resolution and
Hi Michael,
You might have seen through the relax-comm...@gna.org mailing list
messages that I have recently updated the relax website
(http://www.nmr-relax.com). As part of the changes, I have modified
your text about the GUI on the relax features webpage
(http://www.nmr-relax.com/features.html#
very small and tau_m < 5ns)
4.) Model-free analysis within relax GUI
* imported all relaxation data as described
* CSA, bond length values: default values taken
* unit vectors from 1AEY.pdb (averaged in relax)
All the relax data of this run including the results files and consistency
testing p
Hello all,
I was using the GUI version of the software to run the tutorial available
in the manual for analysis of relaxation dispersion.
When i execute the run I get the following error
RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (Mon Nov 17
10:50:08 2014)' already exists.
Not
Hi Lora,
Welcome to the relax mailing lists! For the problem you are seeing,
do you mean that the spin viewer window (i.e. via the main menu
View->Spin Viewer) cannot be resized? Or the spin loading wizard when
clicking on the 'Load spins' button or selecting 'Load spins' from the
right-click po
ch 31, 2015 2:31 AM
To: Lora Picton
Cc: relax-users@gna.org
Subject: Re: relax gui - window resize issue
Hi Lora,
Welcome to the relax mailing lists! For the problem you are seeing,
do you mean that the spin viewer window (i.e. via the main menu
View->Spin Viewer) cannot be resized? Or
gt; Sent: Tuesday, March 31, 2015 2:31 AM
> To: Lora Picton
> Cc: relax-users@gna.org
> Subject: Re: relax gui - window resize issue
>
> Hi Lora,
>
> Welcome to the relax mailing lists! For the problem you are seeing,
> do you mean that the spin viewer window (i.e. via the
sing of all spectra: Bruker TOPSPIN 3.1
> * peak picking with CCPN 2.2.1:
> o T1, T2 (pseudo-3D) picked with „Follow intensity changes“ function
> o HetNOE (2D planes) picked with „Heteronuclear NOE“ function
> * T1, T2 analysed with relax' fitting function
> * consisteny t
27;, force=True)
Exception raised in thread.
Traceback (most recent call last):
File "/usr/local/relax/gui/analyses/execute.py", line 88, in run
self.run_analysis()
File "/usr/local/relax/gui/analyses/auto_model_free.py", line 765, in
run_analysis
dauvergne_prot
nd=None, colour_list=None, file=None,
> dir='/faust/TENSOR/sh3_EdA/final/pymol', force=True)
> Exception raised in thread.
>
> Traceback (most recent call last):
> File "/usr/local/relax/gui/analyses/execute.py", line 88, in run
> self.run_analysis()
>
gt; relax_data.delete(ri_id='noe.600')
Traceback (most recent call last):
File "/usr/local/relax/gui/interpreter.py", line 311, in run
apply(fn, args, kwds)
File "/usr/local/relax/prompt/relax_data.py", line 128, in delete
relax_data.delete(ri_id=ri_id)
File &
c user
functions which would do what you need (and maybe even try to add them
yourself).
> Also, deleting NOE data sets is failing here:
>
> relax> relax_data.delete(ri_id='noe.600')
> Traceback (most recent call last):
> File "/usr/local/relax/gui/interpreter.py",
Hi Edward,
On 05.06.2012, at 15:48, Edward d'Auvergne wrote:
> Reading my thesis
> (http://www.amazon.com/Protein-Dynamics-Model-free-Analysis-Relaxation/dp/3639057627)
> might be easier :P
I have to admit, I underestimated the amount of math knowledge which is needed
to understand (and trouble
On 08.06.2012, at 12:04, Martin Ballaschk wrote:
> It may well be that the NMR structure (1aey, from 1997!) does not reflect
> reality well enough. At the moment relax is giving the crystal structure
> (1shg, even older) with artificially added protons (Amber), and I'm hoping
> that it'll yiel
Hi Prem,
Welcome to the relax mailing lists! For the problem you are seeing,
could you please create a bug report for this
(https://gna.org/bugs/?func=additem&group=relax)? Cheers! It would
be good to know what steps you took to encounter this bug, and where
in the analysis the problem occurred
Dear Prem.
Welcome to the mailing list!
I guess that you mean the manual at:
http://www.nmr-relax.com/manual/Contents.html
The relaxation dispersion auto-analysis in the GUI
http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html
Where the test data is in:
test_s
Hi Prem.
I added the tutorial here:
http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI
I tried to take power of the scripting, to get around the tedious work on
defining the experiment settings for all spectra.
So this script should take you to the "end po
Hi Troels and Prem,
Troels, for a suggestion for improving the script in your tutorial,
you could use:
"""
from time import asctime, localtime
pipe_bundle = "relax_disp (%s)" % asctime(localtime())
pipe_name = "origin - %s" % pipe_bundle
"""
This is how the new analysis wizard in relax creates
Hi Troels,
For the tutorial at
http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI
, I would suggest also adding that relax can be run using OpenMPI to
speed up the relaxation dispersion analysis. So that if you have a
machine with 8 cores and OpenMPI and pyt
Hello Troels and Edwards,
The modified tutorial that you sent me worked fine.
Looks like I might have done some mistake while setting up the run using
the original GUI tutorial for relaxation dispersion. I will try the
original tutorial again to make sure the setup was fine. if the error still
pop
Hello Edward and Troels,
I will take a look at the suggestion and try again. This is the first time
I am using the program for relaxation dispersion analysis. I will also go
through the tutorial one more time to make sure that I went through all the
steps. I will also create the bug reports and se
Hello Edward,
I tried the GUI version of the setup again for the relaxation dispersion
(on the test data) and it ran without any error this time. Its possible I
made some mistake during the setup thr last time.
Thank again for the help
Prem
On Tue, Nov 18, 2014 at 5:27 AM, Edward d'Auvergne
Hi Prem,
From the error message, this is within the automated analysis for
relaxation dispersion. Creating the data pipe 'R2eff - relax_disp
(Mon Nov 17 10:50:08 2014)' can only happen once, as the 'R2eff' model
is only optimised once (there is a loop over all models). There is
only one thing I
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