Hi Hongyan,
I've just come back from summer holidays at the beach which is why I
didn't respond to your earlier queries. Chris answered your questions
exactly as I would have. relax has been designed to be flexible. The
user functions and the scripting abilities allow you to implement
almost all of the different model-free data analysis chains present in
the literature - and there are many! The only limitation is your
imagination.
The chi-squared and parameter value differences you are experiencing
are due to a multitude of factors. Breaking these into the different
aspects of the data analysis chain, these are: model selection, model
elimination, and optimisation (or minimisation). By carefully
redesigning your relax script, you should be able to replicate very
similar behaviour to Art's Modelfree (or Dasha if you wish). I
wouldn't recommend that at all though (see below). Douglas Kojetin
has asked the same question
(https://mail.gna.org/public/relax-users/2006-12/msg00008.html,
Message-id: <ACA2792B-32AE-4DE0-987C-8877E35E2AF8@xxxxxxxxx>) and
Chris MacRaild's response
(https://mail.gna.org/public/relax-users/2006-12/msg00011.html,
Message-id: <1166697626.7569.122.camel@mrspell>) as well as my
response in that thread explains all the differences in fine detail
(https://mail.gna.org/public/relax-users/2006-12/msg00017.html,
Message-id: <7f080ed10612210815i4e2b8010we9fdb80f0fd89560@xxxxxxxxxxxxxx>).
I hope these archived posts help (I'd recommend reading them all).
Cheers,
Edward
On 1/8/07, Hongyan Li <hylichem@xxxxxxxxxxxx> wrote:
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
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Re: scripts