Dear Yitao,
Welcome to the relax mailing lists! My late response is because I
have just returned from holidays. To simplify how you use relax, you
could try running the relax graphical user interface or GUI
(http://www.nmr-relax.com/refs.html#Bieri11):
Bieri M., d'Auvergne E. J., Gooley P. R. (2011). relaxGUI: a new
software for fast and simple NMR relaxation data analysis and
calculation of ps-ns and μs motion of proteins. J. Biomol. NMR, 50(2),
147-155. (http://dx.doi.org/10.1007/s10858-011-9509-1)
At the command prompt, just type:
$ relax --gui
This works on all operating systems. How do you wish to perform your
model-free analysis? You should note that there are two parts to a
model-free analysis. The first part are the basic model-free models
to be optimised as well as the diffusion tensor. The second part is a
highly iterative protocol for how you should solve the combined and
convoluted optimisation and model selection problem. See my review at
http://dx.doi.org/10.1039/b702202f for an in depth explanation of this
dual concept.
There are a number of protocols available for model-free analysis.
Almost all can currently be implemented via a relax script using a
little Python programming, if you have the ability. However one
protocol is already fully implemented for you. This is the new
protocol I published in:
d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494. ( http://dx.doi.org/10.1039/b702202f)
d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology for the dual optimisation of the
model-free parameters and the Brownian rotational diffusion tensor. J.
Biomol. NMR, 40(2), 121-133.
(http://dx.doi.org/10.1007/s10858-007-9213-3)
If you read these two references, which I highly recommend you do, you
will see that ideas from the Peter Wright 2004 JBNMR paper are no
longer relevant. As the new protocol starts with the internal motion
rather than with the diffusion tensor - you do not need an initial
diffusion tensor estimate. So all of the extensive literature on
correctly finding the initial tensor estimate is no longer of any use.
If you use the dauverge_protocol auto-analysis in a script or simply
use the GUI, then you will be using this new protocol and you can skip
the ideas from the Wright paper. I hope this helps.
Regards,
Edward
On 8 August 2014 06:00, FENG yitao <chemfyt@xxxxxx> wrote:
Dear relax users,
I am a new user of the relax and I don't have any background about
python.
This software seems quite powerful but difficult for me to use. I have
collected the T1, T2 and NOE data. Before sending for modelfree
calculation, I want to select models residue per residue in order to
improve the fitting accuracy as mentioned in P. E. Wright's J.Biomol.NMR
paper in 2004 (model-free analysis of protein dynamics: assessment of
accuracy and model selection protocols based on molecular dynamics
simulation). So I go to the user manual and after several days I got to
know how to input the R1, R2 and NOE data (sorry for my slow learning).
When I start to do model-selection, the software needs me to provide
diffusion tensor but I don't know how to do this. I wonder whether any
of
you have any protocol for easy usage of model selection. I'm sorry for
my
silly question and I am looking forward to your reply.
Best,
Tom
Best,
Yitao
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Re: model selection