Hi, In relaxation data analysis, you can only view the components of the Brownian rotational diffusion tensor that the XH bond vectors sample. So if your macromolecule diffuses as a prolate spheroid but the XH bond vectors are close to perpendicular to the unique axis of the tensor, the only component of the diffusion tensor that the relaxation data contains information about is the eigenvalue Dper (the perpendicular component of the tensor). The result is that the diffusion will appear to be spherical where Diso has the value of Dper! In relax the parameters tm (which is essentially Diso) and Da are optimised. For this case, Da (and hence Dratio) would be undefined - it can have any geometrically possible value while having zero effect on the results.
Have you tried starting with the calculated Da value (or Dratio if you wish)? This is not possible using the 'full_analysis.py' script, but the other sample scripts can be modified to do this. As these parameters will be statistically undefined, the final optimised values should be pretty close to the input values. This assumes tm (or Diso) is set to be close to the Dper value as the curvature of the space may cause optimisation to shift Da. The parameter Dr would also be undefined and this would fully explain the Dr value of 1 reported in bug #7297 (https://gna.org/bugs/?7297). The problem of the undefined Da and Dr, and hence the molecule appearing to diffuse as a sphere, could be resolved by having a few vectors which deviate from the perpendicular. However this is only important if you are actually interested in characterising the Brownian rotational diffusion. In any case, attempting to optimise these values using relaxation data of perpendicular XH's will only result in statistically insignificant values - it's not statistically possible to pull out these parameters. It is almost guaranteed that AIC model selection will select spherical diffusion. Would the ribose CH's together with the base XH's adequately sample three-dimensional space? I hope this info helps, Edward On 10/5/06, Alexandar Hansen <[EMAIL PROTECTED]> wrote:
Hello all, In studying RNA you run into a number of limiting factors of your data set. a) NH data is available only on half of the residues (G's and U's), b) these G's and U's must be in a helix, or the NH becomes exchanged with solvent, and c) the NH vectors on the bases in a helix don't sample space randomly and are oriented ~perpindicular to the diffusion axis (RNA is almost always prolate shaped). This last scenario, for you protein folks, would be similar to the situation where you had a single alpha helix and only NH data, ie. sample only directions paralell to the helix axis. With this in mind, one can easily imagine that any relaxation analysis would be happy to fit them to a lower diffusion model, such as spherical, than what is in reality highly anisotropic. What I'd like to know how to do is impose additional limits on the minimization step such that, for instance, the Dratio could be fixed between some values. With the data I've been analyzing, relax happily fits my NH data to the spherical case and, for the prolate model, fits the Dratio to 1 -> 1.1. From hydrodynamic simulation, we know, however, that the Dratio should be between 4-5. Are there any thoughts on how to do this? On one level, it appears to be forcing the data into a particular model. But if you can know something about the diffusion parameters or anything else a priori from a different source than NMR, shouldn't that be allowed to factor into the analysis? Thanks, Alex Hansen _______________________________________________ relax (http://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://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
