Hi Mengjun, Could I ask you to send the message again? To properly resend a message, please go to my original message, click on 'reply-to-all', and then write a new message (copy and paste the text of your missed message if you wish).
Cheers, Edward On 7 September 2012 11:10, <[email protected]> wrote: > Quoting Edward d'Auvergne <[email protected]>: > >> Hi Mengjun, >> >> Sorry in advance, but the following is the standard pre-composed >> response to a post not sent to the relax mailing lists and not >> labelled as private. If you would like to start a private >> conversation about relax, please label your message as such. If you >> really must start a private exchange, please respond to this message >> saying so. If your message was meant to be sent to the relax mailing >> list, please send the message again. For this, please copy-and-paste >> your message, replying to the original (i.e. no forwarding), and >> making sure that the mailing list is in the CC field by clicking on >> 'reply-to-all'. >> >> Cheers, >> >> Edward >> >> >> >> On 6 September 2012 23:14, <[email protected]> wrote: >>> >>> Dear Dr. Edward d'Auvergne, >>> >>> Thank you very much for your detailed explanations. There are some bugs >>> when >>> I try to import T1 demo.txt from bruker dynamic center to Relax, and I >>> have >>> submit it online. >>> >>> I remembered you said Relax Gui can not perfom model free analysis with >>> only >>> single field strength nmr data, how about the Relax script mode ? I have >>> just read the Relax user messages, the similar questions about single >>> field >>> strength data have been asked before. >>> >>> Thank you very much. >>> >>> With best regards, >>> >>> Mengjun Xue >>> >>> >>> >>> >>> >>> Quoting Edward d'Auvergne <[email protected]>: >>> >>>> Hi Mengjun, >>>> >>>> I've been looking for the relevant links as we have discussed this >>>> topic a number of times on the relax-users mailing list. One good >>>> reference would be to read all the messages sent by myself, Sebastien >>>> Morin, Alex Hansen, Michael Marlow, and Gary Thompson in the thread >>>> called "CSA & bond length" starting at: >>>> >>>> http://thread.gmane.org/gmane.science.nmr.relax.user/192 >>>> >>>> and continued on the relax-devel mailing list at: >>>> >>>> http://thread.gmane.org/gmane.science.nmr.relax.devel/1115 >>>> http://thread.gmane.org/gmane.science.nmr.relax.devel/1116 >>>> http://thread.gmane.org/gmane.science.nmr.relax.devel/1119 >>>> >>>> I'll keep looking for the other threads which discuss this, as this >>>> was recently talked about, but I cannot find the messages right now. >>>> In summary, for protein backbone NH data you should really use 1.02 >>>> Angstrom with -172 ppm CSA. The value of -160 ppm is from solid state >>>> studies of peptides and is an underestimation for solution NMR. >>>> >>>> There is CSA variability but the amount of variability is highly >>>> debated. Some of Nico Tjandra's estimates of variability might be on >>>> the high side, David Fushman's might be more reasonable. In reality, >>>> no one really knows what the real CSA and bond length values are and >>>> no one has reliably de-convoluted the internal ps-ns dynamics from >>>> these parameters to be able to properly answer this question. >>>> Therefore everyone takes the compromise of 1.02 A with roughly -172 >>>> ppm (the Hall and Fushman average value). There is another school of >>>> thought from the NIH direction of Washington DC which says we should >>>> use 1.04 A with -160 ppm. However this will generally shift the order >>>> parameters higher and closer to one - causing the optimisation >>>> algorithms to have severe problems and failures due to the convolution >>>> of the optimisation space that this results in So it is not >>>> recommended for a model-free analysis - the removal of zero-point >>>> motions concept. As long as you are consistent and know that the >>>> order parameters are a relative concept rather than absolute - then >>>> you can compare different states. I hope this helps. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> P. S. If you do solve this problem reliably, you will probably >>>> receive quite a few citations and make a name for yourself. However >>>> the NMR field has being trying to solve this unsuccessfully for the >>>> last who knows how many decades. So I wouldn't recommend trying >>>> unless you have an incredible amount of spare time and don't mind >>>> diving into the deepest depths of NMR and physics theory. >>>> >>>> >>>> >>>> >>>> On 5 September 2012 18:09, <[email protected]> wrote: >>>>> >>>>> >>>>> Hi, >>>>> >>>>> When doing model-free analysis, NH bond length set to 1.02 angstrom >>>>> normally, but it is a little bit different for different amino acid >>>>> residue; >>>>> and >>>>> also the N chemical shift anisotropy set to say -160 ppm normally, but >>>>> CSA >>>>> is changing from residue to residue, How do Relax solve such kind of >>>>> problem when doing model-free analysis? >>>>> >>>>> Regards, >>>>> >>>>> Mengjun Xue >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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
