Dear Vineet, The problem you are seeing is a simple bug - Dpar is simply being displayed twice. Could you please create a bug report for this? Simply fill out the details at https://gna.org/bugs/?func=additem&group=relax. I will then fix the problem and the solution will be available with the next relax release. The bug report will be useful for other users
Cheers, Edward P. S. I can already see the problem in the relax source code. See if you can see it too in the display() function at http://www.nmr-relax.com/api/3.1/pipe_control.diffusion_tensor-pysrc.html#display. On 14 May 2014 17:00, Panwalkar, Vineet <v.panwal...@fz-juelich.de> wrote: > Dear users, > > I have recently carried out two seperate model-free analysis on a ~5 kDa > protein with relaxation data measured at 600, 800 and 900 MHz. I used the > fully automated analysis scripts for the analysis. > > In the first run, I used the lowest energy structure from my 15 structure > ensemble. I get an oblate diffusion tensor. When I read the results and ask > for diffusion_tensor.display() in relax, I get the table with all the data > which is as follows... > > Diffusion type spheroid > tm (s) 4.63577e-09 > Diso (rad/s) 3.59523e+07 > Da (rad/s) -3.36136e+07 > Dpar (rad/s) 1.35432e+07 > Dper (rad/s) 1.35432e+07 > Dratio 0.287196 > theta (rad) 0.633624 > phi (rad) 2.61738 > Fixed flag True > > What is confusing me is that, even though the Dratio is 0.287196, the > individual Dpar and Dper values are exactly the same! I have seen the same > when I run relax on a complex of the 5 kDa protein and a 1.1 kDa peptide, > where relaxation data was recorded only for the protein. > > I ran another run, this time using the pdb file containing all the 15 lowest > energy structures. Analysis of the same relaxation data with this structure > gives me an ellipsoid diffusion model with following parameters.. > > Diffusion type ellipsoid > tm (s) 4.63094e-09 > Diso (rad/s) 3.59898e+07 > Da (rad/s) 2.4722e+07 > Dr 0.475806 > Dx (rad/s) 1.59863e+07 > Dy (rad/s) 3.9512e+07 > Dz (rad/s) 5.24711e+07 > alpha (rad) 2.59643 > beta (rad) 2.087 > gamma (rad) 0.438009 > Fixed flag True > > I remember reading an old post where Ed mentions that relax is not set up to > carry out analysis for residues with multiple NH bond vectors since it lies > in the model-free theory itself. In the same post it is also mentioned that > if that is the case then relax should give an error. Now, about 5 residues at > the N terminus and 2 at the C terminus of my 43 residue protein are > unstructured and show high backbone RMSD. It would be great if i get some > help regarding the understanding of why in such a case, there was no error > given from relax. And also, what measures are to be taken to run relax > analysis on such a protein using the 15 structure ensemble as an input > structure. Is this change from oblate to ellipsoid a case of over-estimation > of the diffusion properties occuring due to highly flexible termini in the > protein? > > Regards, > > Vineet > > > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-users mailing list > relax-users@gna.org > > 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 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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
