Thank you Edward for your comprehensive explanation! I will look into the literatures you mentioned. Have a good weekend!
Xi Sent from my iPhone On Oct 12, 2012, at 4:55 AM, "Edward d'Auvergne" <[email protected]> wrote: > 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 <[email protected]> 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 >> >> >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-users mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-users >> _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
