Dear Edward,
Thanks for your reply. I have submitted a bug report as requested.
On another note, I wonder if it is possible to modify the nmr-relax programme
so that I can do model-free analysis with data from only one field strength?
Alternatively, do you know of any programme (that can be installed on
Windows) that can do such analysis? My work focused mainly on small molecule
and ligand-based NMR and I have only just very recently started looking in to
protein dynamics so I am still experimentinng different software and data
treatment etc.
Thanks for your time and I hope to hear back from you.
Have a good weekend.
Regards,
Ivan
Ivanhoe Leung
MChem DPhil (Oxf)
Chemistry Research Laboratory
Oxford University
________________________________________
From: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] on behalf of
Edward d'Auvergne [edward@xxxxxxxxxxxxx]
Sent: 07 February 2014 16:27
To: Ivanhoe Leung
Cc: relax-users@xxxxxxx
Subject: Re: Model-free analysis error
Hi Ivan,
Welcome to the relax mailing lists! The problem you are seeing
appears to be a genuine bug in relax caused by incomplete data input.
This is no fault of your own and relax should, in this case, be
presenting you with a window explaining which data is missing. As
this is a relax bug, could you please submit a bug report at
https://gna.org/bugs/?func=additem&group=relax ? That would be
greatly appreciated. It would be very useful if you could attach data
files containing only data for about 2 spin systems (you can randomise
these slightly if you wish to keep them secret). The PDB file could
also be truncated to only include those residues or atoms. All the
truncated files can be attached to the bug report. Then if you could
give a description of every step you take in the GUI to produce the
bug, I should then be able to replicate the bug and fix it within
minutes. I will also be able to use all of your files to create a
'GUI test' which will catch the bug and, when the test passes, I will
then know that the bug is truly and permanently eliminated.
Cheers!
Edward
P. S. The simple solution is that you need to click on the buttons
under the relaxation data list to set up the spin isotope information
and the dipolar and CSA relaxation mechanisms. But if you could
submit the bug report, that would be of great benefit as the bug can
then be squashed!
On 7 February 2014 15:41, Ivan Leung <ivanhoe.leung@xxxxxxxxxxxxx> wrote:
Hi,
This is the first time I use NMR relax for model-free analysis (so apologise
in advance if the answer to my question is trivial). I am using relax 3.1.5
on Windows 8.
Basically I have some R1, R2 and NOE data (that I have fitted elsewhere) and
a pdb file. Using the spin editor I have loaded N, C, H from the pdb file.
I have also added three relaxation data lists for my R1, R2 and NOE data.
The relaxation data were saved as .txt files. The format of the data is as
follows "residue no., residue type, R1/R2/NOE, spin type":
2 ALA 5.49631746729691 N
3 ASP 3.74279511939516 N
4 ASP 6.12594952217594 N
6 SER 6.75812664729337 N
I then press execute. The programme successfully read the sequence and my
R1/R2/NOE data. However, then I receive the following error message
Traceback (most recent call last):
File "C:\Users\ivanhoe.leung\Desktop\relax-
3.1.5\gui\analyses\auto_model_free.py", line 588, in execute
data, missing = self.assemble_data()
File "C:\Users\ivanhoe.leung\Desktop\relax-
3.1.5\gui\analyses\auto_model_free.py", line 416, in assemble_data
if spin.isotope in ['15N', '13C'] and (not hasattr(spin, 'csa') or
spin.csa == None):
AttributeError: 'SpinContainer' object has no attribute 'isotope'
It would be appreciated if you can shed some light into my question -
whether I missed some obvious steps or if my data format is not correct.
Thanks
Ivan Leung
MChem, DPhil (Oxf)
Postdoctoral research assistant
Department of Chemistry
University of Oxford
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RE: Model-free analysis error