Hi Sean,
Welcome to the relax mailing lists! I'll start by explaining how
relax can handle your single field strength data. Firstly, I need to
point out that relax can do everything Modelfree4 does and it can
replicate the results of Modelfree4 exactly (well, almost, as real
constraint algorithms are used in relax and that used by Modelfree4
will never be added to relax). I used this replication of Modelfree4
and Dasha behaviour as the basis for my 2008 papers
(http://dx.doi.org/10.1007/s10858-007-9214-2,
http://dx.doi.org/10.1007/s10858-007-9213-3), for understanding why
these two softwares produce sometimes quite different results. I
don't think this was mentioned in the papers or supplement as is it so
basic in relax to do - you simply pick the same optimisation algorithm
as the other software and decrease the optimisation precision and
maximum number of optimisation iterations to match (see table 1 of the
first paper for these).
So, to perform your analysis, you need to note the difference between
the theory and optimising the model-free models verses a full analysis
protocol. These are very different and it confuses a lot of people.
The former is fast and only takes minutes to an hour. The later is
super-iterative and much slower, taking a day to 1-2 weeks. There is
a lot of software out there that implements the former (Modelfree4,
Dasha, Tensor2, DYNAMICS), and then you are expected to manually take
the steps required for fulfilling the full protocol yourself (some
people don't know this and end up publishing very questionable
dynamics). So what are the protocols? The first full protocol was
published in the Mandel et al, 1995 paper:
http://www.nmr-relax.com/manual/The_methodology_of_Mandel_et_al_1995.html
When implemented correctly, this takes an incredible amount of time as
expensive Monte Carlo simulations are performed at each step and each
model to obtain the chi2 and F-test statistics. As I published in my
2003 model selection paper
(http://dx.doi.org/10.1023/A:1021902006114), this should not be used.
This introduces, deliberately I should note, or the original paper
notes, bias towards the simpler models and hence less motion. Another
major problem is the F-test. The F-test is useful for comparing
models, but there is fine print the most people don't know about. The
F-test is only statistically valid when the two models compared are
nested! This is mentioned in the Numerical Recipes book series, for
example. As The next protocol I designed based on this one and it
handles single field strength data:
http://www.nmr-relax.com/manual/The_diffusion_seeded_paradigm.html
It is similar in that you need and initial diffusion tensor estimate.
However it replaces the chi-squared, F-tests, and chi-squared value
empirical cut-offs with statistical AIC model selection, introduces
the concept of model elimination
(http://dx.doi.org/10.1007/s10858-006-9007-z), removes the need for
intermediate Monte Carlo simulations, and simplifies the flow of
operation. The last protocol I'll mention here is the one I devised
to eliminate the problems associated with the initial diffusion tensor
estimate:
http://www.nmr-relax.com/manual/The_new_model_free_optimisation_protocol.html
http://www.nmr-relax.com/manual/Model_free_analysis_in_reverse.html
This is the protocol from my second 2008 paper
(http://dx.doi.org/10.1007/s10858-007-9213-3). If you are using the
relax model-free auto-analysis (called the dauvergne_protocol, see
http://www.nmr-relax.com/api/3.3/auto_analyses.dauvergne_protocol-module.html)
or the graphical user interface (GUI), you will be using this
protocol. I have implemented it as a fully automated auto-analysis
which is essentially just a complicated relax script. Although this
protocol solves all of the earlier problems with model-free analyses
(protocols), it absolutely requires data at two fields.
So, how do you implement the protocol of
http://www.nmr-relax.com/manual/The_diffusion_seeded_paradigm.html for
single field strength data? I have answered this many times on the
relax mailing lists, and it has been summarised in the following relax
wiki article:
http://wiki.nmr-relax.com/Model-free_analysis_single_field
You will find the links to the discussions there highly informative!
For the protocol described therein, most steps are present as
individual scripts in the sample_scripts/model_free/ directory. I
have not merged these together into an automated analysis yet, mainly
due to the horrendous artefacts of using single field strength data
that are often interpreted as real dynamics. The first step is to
obtain the initial diffusion tensor estimate. There is no script for
this as most people use Tensor2 for this. Neither Modelfree4 nor
Dasha implement this. However this is not ideal as there is no clear
mapping of the spherical angles and Euler angles between Tensor2,
Modelfree4, Dasha, DYNAMICS, and relax (due to lack of documentation).
For the rest, I'll let you read
http://wiki.nmr-relax.com/Model-free_analysis_single_field#Protocol.
For the problems associated with single field strength data, see
http://wiki.nmr-relax.com/Model-free_analysis_single_field#Warning.
Don't hesitate to ask if you have any questions.
Regards,
Edward
On 11 December 2014 at 03:26, Sean Leo Moro <smoro@xxxxxxx> wrote:
Hello Users,
I am new to the world of model-free analysis, I have my first data set of
R1, R2, and NOE at 800mHz, at 35C and 50C. I would like to use relax as the
program for analysis, as it seems both robust and user-friendly.
Unfortunately, it would be quite difficult for me to acquire data at a
lower field since my protein is ~40kDa and the fact that the 600mHZ
spectrometers at my university can only decouple, but not detect, 15N.
I am curious, what catastrophic event would occur if I were to try to use
relax with only data sets from 800mHz? I've read through the references,
but could someone make it abundantly clear to me why this is a horrible
idea? Otherwise, I will have to use modelfree, and after reading through
the d'Auvergne/Gooley 2008 J Biomol NMR papers, I feel like that won't be
so great either.
Thank you,
Sean Moro
PhD candidate
University of California, Irvine.
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Re: What happens if I try to do MF analysis only having 800mHz data?