Hi Edward, Thank you for the fast (as always) response.
The order of the calculation is the following: 1. Model-free fitting using an estimated diffusion tensor with "mf-multimodel.py". 2. Model selection with "modsel.py". 3. Diffusion tensor optimization (first output). Chi2 = 167.466849 4. Adjustment of the diffusion tensor in "mf-multimodel.py" to the one in #3. 5. Model-free fitting as in #1 (second output). 6. Model selection as in #2. Chi2 = 166.606795 I am using the repository version. I am not sure about the exact revision, but the last update I made was about 2 weeks ago. My first guess was just as yours, that the tensors are identical and the angle difference is just due to symmetry, but it does not seem to be the case. I can forward the two pdbs if it will help. Vitaly On Mon, Jan 23, 2012 at 11:20, Edward d'Auvergne <[email protected]> wrote: > Hi Vitaly, > > Do you mean that if you start with two different starting points, you > end up with two different tensors? For the different rounds of > iterations do you mean from the dauvergne_protocol.py script? Are the > chi-squared values the same in both? There might also have been a fix > for the diffusion tensor representation in more recent relax versions. > Are you using the newest 1.3.13 version? Running 'relax -i' will > give all the version info. There are symmetries in the diffusion > tensor space, so two {theta, phi} pairs with different values can > represent exactly the same tensor. Though the different tensors are > very strange, especially considering that the tm and Dratio values are > essentially identical! Are you using Modelfree4 as a back end > optimisation engine? > > Regards, > > Edward > > > On 23 January 2012 18:03, V.V. <[email protected]> wrote: >> Dear Edward, >> >> I have encountered strange behavior with the initialization of the >> diffusion tensor. I ran the first round of iterations, ending up with >> the following oblate tensor: >> >> =============================== >> Alternate parameters {tm, Dratio, theta, phi}. >> tm (s): 9.486979075650368e-09 >> Dratio: 0.6141733435119592 >> theta (rad): 3.64621046835412 >> phi (rad): 1.9625997908540063 >> =============================== >> >> For the next round of model-free optimization, I have specified these >> parameters manually: >> >> =============================== >> diffusion_tensor.init((9.486979075650368e-09, 0.6141733435119592, >> 3.64621046835412, 1.9625997908540063), param_types=2, >> spheroid_type='oblate', fixed=True) >> =============================== >> >> Yet in this round the diffusion tensor was showing up with different >> Theta and Phi angles: >> >> =============================== >> Alternate parameters {tm, Dratio, theta, phi}. >> tm (s): 9.486979075650368e-09 >> Dratio: 0.6141733435119593 >> theta (rad): 0.0636383778934639 >> phi (rad): 0.0342538282493545 >> =============================== >> >> I have generated pdbs of both tensors and they are not identical. Do >> you have any suggestions what is causing this? >> >> Thank you, >> Vitaly _______________________________________________ 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
