Re: diffusion tensor related -- January 17, 2007 - 02:45

I have tried to use "diffusion_tensor.init(name, (6.77e-9, 0.8, 80, 300),
param_types=2, spheroid_type='prolate', fixed=1)" in mf-multimodel.py script,
the tensor was obtained from r2r1_diffusion, I supposed that tensor should be
fixed, but when I checked results from relax, both theta and phi have been
changed. Why?

Cheers!

Hongyan

Quoting Chris MacRaild <c.a.macraild@xxxxxxxxxxx>:

> On Fri, 2006-12-29 at 12:12 +0800, Hongyan Li wrote:
> > Dear relax users,
> > I am trying to run relax using spheroid model. I am a bit confused how to
> set
> > diffusion tensor. I tried r2r1_diffusion to get Diso and Dper and Dpar,
> Theta
> > and Phi, then input these values into the script
> (sample_script/model-free.py)
> > and in this script "diffusion_tensor.init(name, (2e-8, 1.3, 60, 290),
> > param_types=0, spheroid_type='prolate', fixed=1)" I guess the values 
> > should
> be
> > tm and Da, theta and Phi (is the second value 1.3 Da? seems not right 
> > cause
> I
> > got 5e7 for this)
>
> It looks to me like this line in model-free.py was not properly updated
> when the diffusion_tensor.init() function was changed in relax a few
> versions back. The line should read:
>
> diffusion_tensor.init(name, (2e-8, 1.3, 60, 290), param_types=2,
> spheroid_type='prolate', fixed=1)
>
> ie. the value 1.3 is actually Dr (= Dpar/Dper), not Da
>
> Sorry for the confusion.
>
> The full set of possible parameter sets and their corresponding
> param_types values are described in the documenation for this function
> (do help(diffusion_tensor.init) at the relax prompt, or look at the
> manual)
>
> >  what do the flages mean? I tried to change param_types=0 to
> > 1, relax will require me to change tm to Diso. Again if I change fixed 
> > from
> 1
> > to 0, relax will encounte problems with GridsearchSize too big error and
> stop.
> > How should I set the diffusion tensor?Does it means if fixed=1, the
> diffusion
> > tensor I input should be fixed? But I checked results that the Theta and
> Phi
> > still varied.
>
> The fixed flag simply defines whether or not the diffusion tensor can be
> varied during optimisation. This can be changed later using the fix()
> command. Grid searches will fail unless the diffusion tensor is fixed
> due to the dimentionality of the search space.
>
> Chris
>
>
> > I would be very much appreciate any suggestions!
> >
> > Hongyan
> >
> > Dr. Hongyan Li
> > Department of Chemistry
> > The University of Hong Kong
> > Pokfulam Road
> > Hong Kong
> >
> >
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Dr. Hongyan Li
Department of Chemistry
The University of Hong Kong
Pokfulam Road
Hong Kong