Hi Soumya, The issue you are seeing is often due to diffusion tensor problems. In most such cases, the simple assumptions that the diffusion tensor is spherical, spheroidal, or ellipsoidal does not hold. Are you working with a single domain globular protein? Could you be experiencing partial dimerisation?
Without some of the graphs or more information, it is a little hard to understand what could be happening. Ideally plots of the R1, R2, and NOE data at both fields, together with an S2 plot would be needed. And the final diffusion tensor values. If you would like to communicate this information, you could create a support request using the link https://gna.org/support/?func=additem&group=relax and attach the plots there. But keep in mind that this information will be forever public, so maybe you would like to abstract away some of the information (figures in PNG form, no numbers directly given, etc). Note that for the publication, you really should deposit the final results to the BMRB to make the information publicly available anyway (click on "File->Export for BMRB deposition" in the GUI for easy BMRB file creation). Another issue could be data inconsistency. Both fine temperature control and calibration on a per experiment basis are essential for obtaining reliable relaxation data. This is described in detail in the relax manual in the relaxation curve-fitting chapter (for example at http://www.nmr-relax.com/manual/Temperature_control_calibration.html). You can use Sebastien Morin's consistency testing analysis in relax to see if you have any data inconsistencies. See the relax manual for details (the PDF is of much higher quality http://download.gna.org/relax/manual/relax.pdf, but the HTML version is at http://www.nmr-relax.com/manual/Consistency_testing.html). Regards, Edward On 25 February 2014 09:03, Troels Emtekær Linnet <[email protected]> wrote: > Dear Soumya. > > Would you be able to provide the script you have used for the analysis? > Or did you use the GUI? > > That could help find possible "errors". > I guess that it would be something similar to: > http://www.nmr-relax.com/manual/Single_model_free_model_script_mode_sample_script.html > > If you have saved the output from relax prompt, I have tried to make a > grep script that convert the > output to a relax script. > http://wiki.nmr-relax.com/Grep_log_file > > Best > Troels > > 2014-02-25 7:25 GMT+01:00 Soumya Joseph <[email protected]>: >> Hi, >> >> I've conducted model-free analysis using the default protocol set up in the >> GUI on a protein for which I have data recorded at 600 and 800 MHz. The >> order parameters in s2.txt look very strange: regions I know are dynamic >> have larger S2 values than those in the "structured" regions. My >> understanding is that if the value is close to zero then it is highly >> dynamic and if close to 1 => very rigid. My results are the inverse of what >> I'm expecting. The calculation ran without any errors and I've checked the >> input data for any obvious errors. Has anyone come across this before? >> >> Another strange thing is that the regions I know to be structured (which >> seem to have small S2 values) have very large associated errors. The N- and >> C-termini of my protein however have higher S2 values but have smaller >> associated errors. >> >> Does any one know what could have happened? >> >> Cheers, >> Soumya >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 _______________________________________________ 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
