HI Xi Huang,
Your question is quite good one. The bond vector orientation is quite
important and if your input structure does not have the vectors in the
average orientation, you will start to see artificial motions. I
would recommend you to read 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).
This talks about the artificial motions that arise dependent on the
diffusion tensor anisotropy and rhombicity - both the artificial
nanosecond motions of the Schurr 94 paper and the artificial Rex from
the Tjandra 96 paper. This review also points to all the relevant
literature (note there is not much at all).
One problem with current model-free theory is that a single, averaged
bond vector orientation is assumed. Therefore it is quite important
to have a good starting structure. As I have discussed in my second
2008 paper (http://dx.doi.org/10.1007/s10858-007-9213-3 I think,
though maybe it was the 2007 paper), I would recommend comparing the
dynamics you see from the final results to that of the local tm
models. This is a good test of consistency (in a way complementary to
Sebastien Morin's relaxation data consistency testing analysis in
relax), but be aware that the local tm models are sometimes not very
stable (the tm value can sometimes head off to weird values). I would
also run the model-free analysis on a number of your structures and
simply compare. If you use Gary Thompson's multi-processor code built
into relax and have access to a multi-core, multi-cpu, or clustered
systems, then you should be able to blast many, many structures
through and compare the results. I hope this information helps.
Regards,
Edward
P. S. If you manage to theoretically solve and eliminate this bond
vector problem from the base model-free theory, that would be quite an
achievement and one very impressive paper!
On 8 October 2012 18:02, Xi Huang <huangxi987412@xxxxxxxxx> wrote:
Hi Edward,
The protein I am working with has several conformations and the exchange
rate is in around 100micro seconds timescale. I am wondering when I choose
different pdb structure as an input file to "relax", how big the final
result (S^2) will differ from each other? Is there any literature talking
about the influence of choosing structure coordinates?
Thanks for your help
--
Xi Huang
PhD Candidate, Division of Physical Chemistry
Gail E. Fanucci Research Group
Department of Chemistry
University of Florida
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Re: How big the influence of pdb structure on final result