Hi, Please see below for my replies.
On Fri, Mar 28, 2008 at 2:59 PM, Carl Diehl <[EMAIL PROTECTED]> wrote: > Hi. > I used the full_analysis.py script for testing and evaluating relax in > comparison with published data. > > The system was calcium-loaded Calbindin D9k, with R1 & NOE at 600 MHz > and R2, R1 & NOE at 500 MHz. The relaxation data is of very high > quality. The model selection was done using home-written software, so no > ordinary model selection à Modelfree. What do you mean by model selection? Did you use a different technique from the statistical field of mathematical modelling and model selection? Did you use a frequentist method, a Bayesian method, or hypothesis testing methods (the last of which is described in textbooks from this field of knowledge as being very, very bad)? Did you use this to select between model-free models, diffusion models, or the combined global model (model-free + diffusion)? > After running full_analysis.py (removing excess models), By 'removing excess models', do you mean eliminating failed models? What is an excess of models? > model selection > gives me local_tm as the best model for the diffusion tensor. Previous > calculations (both 15N and 13C relaxation data) indicates that the > diffusion tensor is to a good approximation, isotropic (only a very > slight anistropy). What does 'good', 'slight', etc. really mean? For a mathematical modelling perspective, I don't understand these. Is a Da of 1.001+/-0.001 slight, or 1.2+/-0.01, or 1.6+/-0.3? From my experience, my opinion is that unless all the bond vectors point in the same direction, isotropy will never be statistically significant over the spheroids and ellipsoids. > Looking at the local_tm values for the secondary structure, most of them > have a local_tm which is similar to the isotropic tensor. If you used AIC or BIC model selection between the two models, what are the chi-squared values, criteria values, and parameter numbers for each model? In the test, did you compare the local_tm model to the isotropic model? Or did you compare the local_tm model to the isotropic, 2 spheroids, and ellipsoid simultaneously? Again, what is the qualifier most? And how do the non-conforming residues not conform? > Is the local_tm model always correct? For a well folded protein, one > would expect that the local_tm model should be invalid? As this is mathematical modelling, there is no such thing as an invalid model. By definition of the term model, a model is an approximation of something far more complex. Therefore there is only a grey scale of how good a model approximates reality (of course we can never know what is reality). For a folded, single domain, globular protein (with no significant, floppy loops), then the sphere, spheroids, or ellipsoid should be a good description and the local_tm model will not be selected. Could you reproduce the model selection statistics for all 4? If the local_tm model is chosen, then it is an indication that something is not normal - quite possibly interesting dynamics. Unfortunately, there's not enough information in your post for me to tell you exactly what happened. One point that concerns me is that you only have an R2 measurement at a single field strength. Note that to differentiate between chemical exchange effects (which are scaled quadratically with field strength) and internal nanosecond motions (constant at different fields) and anisotropic tumbling of the molecule (again constant), you really need the R2 collected at 2 fields. But this may not necessarily be the reason you're seeing the local_tm model being selected. I'm sorry that I am not yet able to give you a clear answer. Cheers, Edward _______________________________________________ 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
