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 <[EMAIL PROTECTED]>: > 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 > > > > > > _______________________________________________ > > 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 > > > Dr. Hongyan Li Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong _______________________________________________ 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
