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List:       relax-users
Subject:    Re: local_tm model selection
From:       "Edward d'Auvergne" <edward.dauvergne () domain ! hid>
Date:       2007-06-07 8:11:46
Message-ID: 7f080ed10706070111y1cb79097vb8388dd904f091b1 () domain ! hid
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Hi,

If the local tm diffusion model is selected over the spherical, oblate
and prolate spheroids, and ellipsoid then this could be an indication
that your molecule doesn't diffuse as a single globular unit.  A
solution to this could be the use of hybrid models whereby you, for
example, describe two domains using two different diffusion tensors.
Another hybrid would be to describe the system using one of the
diffusion models for most of the spins and then applying the local tm
model to those spins which you think would not be part of the core.
Unfortunately I have not been able to publish this work as of yet.
However these hybrid models are described in my PhD thesis located at
http://eprints.infodiv.unimelb.edu.au/archive/00002799/

Another explanation could be inconsistencies between the relaxation
data sets.  This can happen because of sample heating differences
between experiments and spectrometers.  To overcome these problems, I
use methanol temperature calibration for all experiments, compensatory
blocks of CPMG pulses in the R2 experiment so that each scan has equal
amounts of heating and single scan interleaving for ultimate
temperature normalisation.  Another possible factor could be if two or
more samples are used to collect the data and the protein
concentration is not identical.  Proteins bumping into each other in
the NMR tube is an important factor affecting the global tumbling of
the molecule and changes in the sample concentration can affect the
global tumbling.

Cheers,

Edward

On 6/1/07, Neil Syme <bmbnrs@domain.hid> wrote:
> Using the 'full_analysis.py' script I find that after the 'final' run,
> the diffusion model selected is the local_tm. I have tried removing
> those residues with particularly high or low local_tm values but still
> get the same result. Does anyone ahve any idea why this may be the case?
>
> Thanks,
>
> Neil
>
> ---------------------------------------
> Neil R. Syme
> Institute for Molecular and Cellular Biology
> Astbury Building
> University of Leeds
> Leeds
> LS2 9JT
>
> Email: N.R.Syme04@domain.hid
> Tel: +44 (0) 1133431937
> ---------------------------------------
>
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