Dear Edward,
thank you for your reply. I really missed this discussion on the mailing
list....
The thing is that write now I don't have nor the protein nor the time to
acquire data at a different field....
I'll try to work with what I have...
Thank you again,
Aldino
-----Mensagem Original-----
From: Edward d'Auvergne
Sent: Thursday, September 22, 2011 9:32 AM
To: Aldino
Cc: relax-users@xxxxxxx
Subject: Re: Model-free - 1 frequency
Dear Aldino,
Welcome to the relax mailing lists. You can for sure use relax to
analyse single field strength data, but it is not recommended. relax
will do everything Modelfree4 and Dasha will do, plus a lot more.
This is not reachable from the GUI though, you will have to implement
this in a special script. There are some sample scripts which partly
implement this (see the sample_scripts directory), but to put together
a full analysis, you will have to do some serious scripting. You have
to do this anyway with Modelfree4 or Dasha, as you have to iteratively
optimise the diffusion tensor and model-free parameters until
convergence (see my paper d'Auvergne and Gooley, 2007
(http://dx.doi.org/10.1039/b702202f) for a review of this procedure,
and d'Auvergne and Gooley, 2008b
(http://dx.doi.org/10.1007/s10858-007-9213-3) for recent advances).
Note that there are many, many issues with using only single field
strength data. These are explained in full detail in my review
(d'Auvergne and Gooley, 2007). The major problem is that the axial
symmetry and rhombicity of the diffusion tensor can be mixed up with
chemical exchange and large amplitude ns motions. With single field
strength data, the difference between the global diffusion and
internal motions can often not be distinguished resulting in either
artificial internal Rex and/or ns motions, or the diffusion tensor is
incorrect hiding the internal motions of the molecule. Only with
multiple field strength data can you distinguish the differences. You
sometimes also need to apply the new methodology in d'Auvergne and
Gooley, 2008b. This is why you will almost never see a publication
with only single field strength data today. Note that using single
field strength data, you have to revert to using the state of the art
from 1995 (see the Mandel, Akke, and Palmer 1995 paper). Your
analysis will be almost two decades behind the current state of the
art (some of this is in the links at
http://www.nmr-relax.com/refs.html). I hope this information helps.
Regards,
Edward
P. S. This has been asked a number of times before. See
https://mail.gna.org/public/relax-users/2008-03/msg00004.html and the
links and threads therein for the past discussions.
On 20 September 2011 16:23, Aldino <aldinoviegas@xxxxxxxxxxxxx> wrote:
Dear all,
I am using the most recent version of Relax to try to calculate some
dynamic
parameters...
The thing is that I only have data at one frequency (600 MHz) and when I
try
to run the model-free calculation it sais that it need 4 or more data
sets...
How can I calculate the model-free parameters with only 3 data sets (NOE,
R1
and R2)?
Thank you in advance,
Aldino Viegas
______________________________________________
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
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Re: Model-free - 1 frequency