Hi Edward,
among various substantial improvements over the available old-school mf
modeling packages, relax implements a different set of model-free models than
e.g. Art Palmer's Modelfree4 or Martin Blackledge's TENSOR2. Neither of the
above programs includes the m0 model (as relax does), where no mf parameters
are determined. You described the m0 model as a special case, where none of
the internal motions / model-free parameters are statistically significant.
Is this equivalent of a "failed" model-free analysis? Does that also mean, in
such a case where relax chooses m0, TENSOR or Modelfree would choose a
nonsignificant model which of course wouldn't be appropriate? Would relax
also choose a model by "chance" if I just left out m0 from the analysis?
I'm not sure what the reason for all parameters being insignificant is and
what the implications are, i.e. what it means in terms of protein mobility.
It cannot mean that the "m0"-residues behave like a static body (S^2 would be
1).
Does it simply mean that the supplied data and models are not sufficient for
the type of motion that the protein is exhibiting? I learned that model-free
works best if the motions are in the extreme narrowing limit, but it is a
misconception that it is limited to this time domain. But aren't there
limitations to the kind of motions that can be modeled by mf?
If the motions approach the NMR timescale, I'd first of all expect broadened
peaks (which I have a lot). From my understanding, that precludes analysis,
but would not be a limitation of the mf formalism itself. These motions could
be picked up by the Rex parameter ... So m0 wouldn't occur if I have amides
moving around at a nanosecond timescale.
I'm also not sure what would happen if the internal motions approach the
global correlation time ...
I don't know if inaccurate or inconsistent data would favor such a behavior.
We now use selective pulses in the R1 and NOE-experiments, temperature
compensatio
Regards
Martin
--
Martin Ballaschk
AG Schmieder
Leibniz-Institut für Molekulare Pharmakologie
Robert-Rössle-Str. 10
13125 Berlin
ballaschk@xxxxxxxxxxxxx
Tel.: +49-30-94793-234/315
Büro: A 1.26
Labor: C 1.10
m0 models