Dear Chris,
Thanks for the helpful suggestion.
I have tried as you suggested to repeat steps 2-4 from estimated tm and then
from best-fit tm. Since estimated tm I used is from modelfree (which is very
good) I actually got converged results immediately. However, I noticed that a
subtle difference in tm caused Chi-square significantly different. Of cause,
other parameters are also different. The question is how to judge which set of
data is more accurate (based on Chi-square??).
Best wishes,
Hongyan
Quoting Chris MacRaild <c.a.macraild@xxxxxxxxxxx>:
Hi Hongyan,
relax is designed to be completely flexible in the way you perform your
analysis, allowing for the procedure to be tailored to the system at
hand, or for new proceedures to be developed. One procedure that I can
recomend which is somewhat similar to the one you outline is as follows:
1. estimate tm
2. fit each residue to dynamic models
3. select best model
4. fit tm and dynamic parameters simultaneously
5. repeat steps 2-4 starting from best-fit tm value. Continue until
results converge
6. repeat steps 2-5 for each diffusion model (isotropic, axially
symetric and anisotropic)
7. select best diffusion model
8. Monte Carlo simulations (error analysis)
As you note, Monte Carlo simulations over all parameters will be very
slow. This is why I recommend only performing the error analysis at the
end of the whole proceedure. I some cases it may be necessary to perform
the Monte Carlo simulations over only the dynamic parameters (ie. with
diffusion tensor fixed) in order to improve efficiency.
There has been some discussion of this and other analysis proceedures on
this list before. The thread that starts here:
https://mail.gna.org/public/relax-users/2006-10/msg00007.html
is worth a look.
Chris
Dr. Hongyan Li
Department of Chemistry
The University of Hong Kong
Pokfulam Road
Hong Kong
Re: scripts