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 relax-users@xxxxxxx 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