The number of 2304 is based the mathematics of Euler angles together with the symmetries in the diffusion tensor space (as I described at http://article.gmane.org/gmane.science.nmr.relax.user/1383 with the 12 axis order combinations, 2 frames of reference - fixed or rotated, 2 rotational directions - forwards and reverse, 2 handednesses, 6 eigenvalue orderings, and 4 rotational symmetries). More information about these different conventions can be found at http://en.wikipedia.org/wiki/Euler_angles together with my paper:
d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119. (http://dx.doi.org/10.1007/s10858-007-9214-2) See for example figure S24 of the supplement for the ellipsoid diffusion tensor symmetries (http://link.springer.com/content/esm/art:10.1007/s10858-007-9214-2/MediaObjects/10858_2007_9214_MOESM1_ESM.pdf). Regards, Edward On 4 February 2013 15:34, <[email protected]> wrote: > Hi Edward, > > Thank you very much for your suggestions, I will read them and the > suggestions at http://article.gmane.org/gmane.science.nmr.relax.user/1383 > more carefully. By the way, the number 2304 (Euler angle combinations) > depends on the pdb file used? Thank you. > > Regards, > > Mengjun > > > > Quoting Edward d'Auvergne <[email protected]>: > >> Hi Mengjun, >> >> Please see below: >> >> >>> I would like to ask you how to display the parameters of disfusion tensor >>> calculated from hydronmr in a pdb file. >> >> >> Firstly, note that you will need to know the format of the parameters >> from hydronmr. There are 2304 Euler angle combinations and you need >> to match the exact 1 with relax to read the parameters correctly! I >> mentioned this before at: >> >> http://article.gmane.org/gmane.science.nmr.relax.user/1383 >> >> Converting to the correct convention is incredibly important and relax >> will not do that for you. Otherwise your tensor will be rotated >> almost randomly in space! >> >> >>> I understand that diff_tensor_pdb.py >>> can do this. >> >> >> This will create a PDB representation of the diffusion tensor and then >> display it in PyMOL. >> >> >>> I understand that results.read(file='results.bz2', dir=None) >>> can read the parameters of tensor optimized in Relax, >>> results.read(file='results.bz2', dir=None) can read the paramters of >>> diffusion tensor from hydronmr? >> >> >> No, the results.read user function is only for relax results files - >> see http://www.nmr-relax.com/manual/results_read.html. >> >> >>> I would like to submit fine the parameters of tensor simulated in >>> hydronmr, >>> and the pdb file, it seems that no files can be submitted under support >>> now? >> >> >> You will need to create your own script, and maybe be a bit creative. >> You can perform all of this in relax, but you will need to discover >> how. As a hint, have a look at the following documentation for >> example: >> >> http://www.nmr-relax.com/manual/pipe_create.html >> http://www.nmr-relax.com/manual/diffusion_tensor_init.html >> http://www.nmr-relax.com/manual/diffusion_tensor_display.html >> http://www.nmr-relax.com/manual/structure_create_diff_tensor_pdb.html >> http://www.nmr-relax.com/manual/pymol_tensor_pdb.html >> http://www.nmr-relax.com/manual/molmol_tensor_pdb.html >> >> I hope this helps. >> >> Regards, >> >> Edward >> >> > > > _______________________________________________ relax (http://www.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
