Dear Dhanas,
Welcome to the relax mailing lists. Thank you, but note that this
program is the work of a number of relax developers. You are correct
that you cannot use the GUI for single field strength data. For such
data, you have to revert to the ancient methodology in the Mandel,
Akke, and Palmer 1995 paper. This will require scripting, but
fortunately most of the scripts are already there for you, just not
fully automated.
To perform this old-style analysis, this will require an initial
diffusion tensor estimate which you can obtain from relax by setting
all spins to model m0 and optimising the diffusion tensors (once for
spherical diffusion, for the prolate spheroid, the oblate spheroid,
and the ellipsoid). This approximates the R1/R2 ratio methods, but
has the advantage of not having to convert between the >2000 Euler
angle conventions/symmetries, etc. which are different between
Modelfree4, Tensor2, Dasha, and relax. Note you cannot simply take a
tensor from one program and use it in another, as all programs use
different Euler or spherical angle notations. There is no sample
script for this, so you will need to write it yourself.
The next part is iterative. You need to fix the diffusion tensor and
optimise the model-free models (i.e. the mf_multimodel.py script).
Then you need to select the best model (the
sample_scripts/model_free/modsel.py script). And finally you have to
optimise the diffusion tensor again (this will require your own script
as there is no equivalent sample script). Using this final diffusion
tensor as a starting point, you need to repeat all the steps of
model-free model optimisation, model selection, and tensor
optimisation until convergence (identical chi-squared values for the
final optimisation).
What you'd like to do will require script editing and writing on you
behalf. You will need extensive use of the user function
documentation in the manual. I do not believe anyone has used relax
to perform such an analysis for a long, long time (I could be wrong
though). Most scripts for this would be for the old relax version
1.0.x or earlier, so they cannot be used with modern versions of
relax. This Mandel et al methodology is heading towards being two
decades old - it is a very ancient technique with many known and
documented problems which you will need to be very aware of! I
suggest starting with my review:
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)
Or my paper:
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).
The review covers most of the problems, and the 2008 paper shows an
example where such methodology clearly fails. To perform a single
field strength analysis, you need to be acutely aware of these
problems. If you have any problems with all of the scripting, please
don't hesitate to ask on the mailing list. I hope this helps.
Regards,
Edward
P. S. Collecting data at 2 or more field strengths (essentially with
both per-experiment temperature calibration and temperature
compensation) will allow you to avoid scripting and use the automated
analysis via the GUI.
On 30 January 2012 19:53, Dhanasekaran Muthu <dhanas.muthu@xxxxxxxxx> wrote:
First, I wanted to thank for creating such a wonderful program for
mode-free analysis. Using the recent version with GUI, I was able to get
T1, T2 and NOE values without much effort. But I am not able to proceed
further to do the mode-free analysis because the relax needs more than one
filed frequency data. My problem is that I have data from only one
frequency and I do not know the sequence of steps involved in running the
relax. I learned from the forum that this has been asked several times and
answered several times. I am also aware of problems with single frequency
data. But I have to work with only one frequency data for the time being.
Even after reading the forum and well-detailed manual, I am not able to
understand what are the steps I should be doing to get model-free data. My
understanding so far is i) first run mf-multimodel.py and then ii)
modesel.py after removing the models M4 to M9. It would be nice if some one
post the details of how to use relax for single frequency data, if they
were successful already running the calculations. I would like to connect
with those people who are in my situation and created successful code for
running relax.
Thanks,
Dhanas Muthu
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Re: Calculations using one magnetic field data