Hi Peixiang,
For your bug report, I am currently downloading and installing a Fedora 18
VM image to test and see if I can replicate the problem. As for the
problem you see with the script, that is because the metadata is not all
set up for the R2eff data. Please have a look at the script at
./test_suite/system_tests/scripts/relax_disp/hansen_r2eff_data.py for a
better idea for how to use this advanced user function. Do you not have
original peak heights/volumes? Is your data measured, or is it synthetic?
If you do have peak intensities, it would be much easier to use as the
relax_disp.r2eff_read* user functions are much more complicated to use
correctly. Also, if you have used Sparky to fit exponential curves, you
should have a careful look at the Sparky 'curvefit.py' file to understand
why you should not use this Sparky feature (a hint is to look at how the
horrible error estimates are obtained).
Note in your log file that you have a number of RelaxWarnings. These
should be very carefully checked, as I can see that there are some rather
fatal ones there. Also note that the data input error checking does not
cover all input data combinations possible when using the
relax_disp.r2eff_data user function. Therefore here the analysis has been
allowed even though you have not specified relaxation times. The result is
that all your spins are deselected:
"""
Deselecting spin ':23@N', the maximum dispersion curve difference for all
curves is 0.0 rad/s.
Deselecting spin ...
"""
There is nothing for relax to do, and hence you see nothing from the grid
search or minimisation.
Regards,
Edward
P. S. Please do not attach files to public mailing list messages. This
results in a lot of strain on the open source infrastructure. The Mailman (
http://www.list.org/) mail server is configured to strip most attachments,
but somehow this attachment made it through. It is better to attach files
to bug reports or support requests at https://gna.org/projects/relax.
Cheers! If the attachment is text, maybe it would then be better to copy
and paste the text into the message itself.
On 3 June 2014 15:27, pma <Peixiang.Ma@xxxxxx> wrote:
Hi, Edward,
Thanks, as your instruction, I tried Gui, but I could not quit selection
relaxation dispersion models. (I just report as a bug)
1) In r2eff_read, I am not quite clear about the pop window. You said I
should load partial experiment ID string as ('%s_%s'%(id,dis_point)).
Then you have the second window to load the file. what does the file mean?
The file is the fitted R2eff or a list for all the R2eff file names?
Is that possible to load a series of files? I guess so, but do you have an
example somewhere?
2) actually, I found script is more powerful, so I just use Troels
mentioned trick. type help(relax_disp.r2eff), then I found the description
about this function.
I made one script, it is included in the log file.
I attached the log file after I run the script.You can see that it reads
all the R2eff value perfectly, but did not do the calculation there.
It is a bit strange to me. . Do you have an idea why?
Do not care too much about the value in the script, such as Grid_inc,
MC_value, they are only for test now.
Peixiang
On 05/30/2014 04:45 PM, Edward d'Auvergne wrote:
Hi Peixiang,
If you do only have R2eff data, i.e. there is no original peak lists,
I'll assume that you would fit into the category of 'power user'. In
this case in the GUI, instead of using the peak intensity wizard via
the spectra list 'Add' button, try the "User
functions->relax_disp->r2eff_read" or "User
functions->relax_disp->r2eff_read_spin" menu entries. You will have
to deselect the 'R2eff' model. Clicking on the 'Execute' button will
then run the analysis.
Regards,
Edward
--
Peixiang Ma, PhD.
Institut de Biologie Structurale (IBS)
UMR 5075 - CEA - CNRS - UJF
41 rue Jules Horowitz
38027 Grenoble Cedex 1, France
Email: Peixiang.Ma@xxxxxx
Re: R1rho RD analysis