Hi, I agree with you, Alex. You're right, this small difference of 2 ppm for the CSA is quite small compared to the real deviation observed experimentally...
However, since few people actually measure the 'real' csa, I think that the best available approximation should be the default and that relax should promote a consistent use, for better comparison between published studies... Also, I think that these default values (for csa and r, for example) should be the same throughout all the relax program, for more consistency... Maybe, in the 1.3 line, these default values should be in a common file so that the jw_mapping and consistency_tests codes (and others if so) could use the same default values. (Maybe this has been discussed before...) Ok. Cheers ! Séb :) Alexandar Hansen wrote: > I'm not a protein expert, but unless you're at ~GHz fields, a 2 ppm > difference in 15N CSA magnitude is going to be negligible. The error > in the site-by-site CSA is going to be ~5-10 ppm, if not more, > anyways. The important thing, I imagine, is that you know what the > value you are using is and what assumptions are involved (ie. > collinearity with NH bond, symmetric CSA tensor). > > Alex Hansen > > > On 7/16/07, *Sebastien Morin* <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Hi, > > It's been a long time since we discussed this (the CSA / bond length > issue in spin relaxation analysis). > > I would agree in using a combination of 1.02 A for bond length and > -172 > ppm for CSA (for 15N-1H vectors). > > Should the default values in the relax code be modified, changing the > CSA from -170 (at least in the jw_mapping code) to -172 ppm ? > > Cheers > > > Séb :) > > > > > Edward d'Auvergne wrote: > > There has been much work describing the importance of the CSA > and the > > bond length. It would be interesting to see how much of a > difference > > measuring the CSA (and the bond length) would make to the final > > dynamic results. As Sébastien said, the 1.04 Angstrom bond length > > should be used with a lower CSA value. My preference though > would be > > to use -172 ppm together with 1.02 Angstrom. > > > > Edward > > > > > > On 9/30/06, Michael S. Marlow <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > >> I agree with the value of -170. Here are my favorite references: > >> > >> Variability of the 15N Chemical Shift Anisotropy in Escherichia > coli > >> Ribonuclease H in Solution > >> Christopher D. Kroenke, Mark Rance, and Arthur G. Palmer, III > >> J. Am. Chem. Soc.; 1999; 121(43) pp 10119 - 10125 > >> "For this data set, the values of are approximately Gaussian > >> distributed with a > >> mean of -172 ± 13 ppm." > >> > >> Protein Backbone Dynamics and 15N Chemical Shift Anisotropy from > >> Quantitative > >> Measurement of Relaxation Interference Effects > >> Nico Tjandra, Attila Szabo, and Ad Bax > >> J. Am. Chem. Soc.; 1996; 118(29) pp 6986 - 6991 > >> Essentially the same value, but identified larger outliers > >> > >> Another aspect of this thread which has not received much attention > >> is the bond > >> length. The refence below suggest 1.04 Angstroms. > >> > >> Determination of Relative N-HN, N-C', C-C', and C-H Effective Bond > >> Lengths in a > >> Protein by NMR in a Dilute Liquid Crystalline Phase > >> Marcel Ottiger and Ad Bax > >> J. Am. Chem. Soc.; 1998; 120(47) pp 12334 - 12341 > >> > >> Mike > >> -- > >> Michael S. Marlow, Ph.D. > >> Department of Biochemistry and Biophysics > >> University of Pennsylvania > >> > >> > >> Quoting Edward d'Auvergne <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>>: > >> > >> > Salut Séb, welcome to the relax users mailing list. Thank > you for > >> > responding Alex. The CSA value is important as the example > shows. > >> > However I would call this a 'fringe' example as it represents > a highly > >> > restricted nanosecond motion. The relaxation data for this > example > >> > was generated by back calculation using the CSA value of -160 > ppm. > >> > Although as Alex pointed out relax is capable of optimising > the CSA > >> > value, I would be wary of these models as they are essentially > >> > untested. I've played around with the models a little and I > have a > >> > feeling that the R1, R2, and NOE values are not sufficient to > tease > >> > out the CSA. To test these models using just the R1, R2, and > NOE at > >> > multiple field strengths, the CSA would need to be accurately > measured > >> > using one of David Fushman's techniques (I'll talk about this > next) > >> > and the values compared to those fitted using the models > built into > >> > relax. > >> > > >> > I believe that the value of -160 ppm was determined by solid > state NMR > >> > of small peptides (it's been a few years since I read the > litterature > >> > on the CSA value in proteins, so I could be wrong). However > a number > >> > of publications have demonstrated that the average CSA value in > >> > solution is higher. I would say that the authorative expert > in the > >> > field is David Fushman. The JACS reference you cite is just > one of > >> > many of his publications on measuring the CSA. He has > demonstrated, > >> > using I think three different techniques now, that the CSA in > proteins > >> > is highly variable. > >> > > >> > Idealy for highly accurate model-free analysis, the CSA value > should > >> > be determined either prior to or during model-free analysis > using one > >> > of his techniques. However most people appear happy to just > set the > >> > CSA value to either the 'ancient' value of -160 ppm or the > solution > >> > average of -170 ppm (David's work again). Using the data you > have > >> > currently collected, I would personally use the value of -170 > ppm. Is > >> > the value of -172 ppm from the Hall and Fushman paper you > cited? I > >> > haven't read that paper yet. > >> > > >> > Edward > >> > > >> > > >> > P.S. I might change the sample scripts to -170 ppm. I had > intended > >> > to change the value a while back but forgot about it. > >> > > >> > > >> > > >> > On 9/30/06, Sebastien Morin <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > >> > > > >> > > Hi again > >> > > > >> > > Thanks for your answer ! > >> > > > >> > > I think that, for me, the CSA value would have a significant > >> impact on my > >> > > analysis since my protein has a tumbling time of about 13 > ns and > >> I have > >> > data > >> > > from 500, 600 and 800 MHz... > >> > > > >> > > I don't know if this is relevant, but I performed simple tests > >> with the > >> > > test data and sample scripts provided with relax (path : > >> > > 'relax/test_suite/data/model_free/S2_0.970_te_2048_Rex_0.149' > >> > > in version 1.2.7 and the sample script 'mf_multimodel.py')... > >> > > > >> > > TEST 1 > >> > > ===== > >> > > r = 1.02 > >> > > CSA = -160 ppm > >> > > m4 > >> > > S2 = 0.97 > >> > > te = 2048 > >> > > Rex = 0.149 > >> > > X2 = 7.3e-28 > >> > > > >> > > TEST 2 > >> > > ===== > >> > > r = 1.02 > >> > > CSA = -172 ppm > >> > > m4 > >> > > S2 = 0.97 > >> > > te = 82 > >> > > Rex = 4.34 > >> > > X2 = 2.27 > >> > > > >> > > As you can see, for this single residue (with data at 500 and > >> 600 MHz), > >> > > there is no effect for the value of S2, but the effect is > >> important for te > >> > > and Rex... And still, the best model (the lower X2) is m4 > for both > >> > > situations... > >> > > > >> > > I think that this ambiguity in the value for CSA leads to > important > >> > > variations in the interpretation of relaxation data. > >> > > > >> > > Thanks for getting me to understand more this topic and also > >> choose the > >> > > best value to use... > >> > > > >> > > Séb > >> > > > >> > > > >> > > > >> > > > >> > > Alexandar Hansen wrote: > >> > > Hi Sebastien, > >> > > > >> > > I'm quite new to relax as well, but I can give you at least a > >> some answer > >> > > to the questions you pose. > >> > > > >> > > In general, the CSA mechanism is a little > underappreciated. At low > >> > enough > >> > > field strengths for 15N relaxation (400-500MHz), the 15N CSA > >> accounts for > >> > > somewhere between 10-20% of your R1 and R2 rates. Varying > the CSA > >> > magnitude > >> > > between 160 and 172 only changes this by 2-3%. So, if > relaxation > >> rates > >> > are > >> > > measured with, let's say, 5% error, there's no statistical > reason > >> to vary > >> > > the CSA. As we go to higher fields (800MHz), the CSA can > account > >> for > >> > 50-60% > >> > > of the R1 and R2 rates and varying the CSA between 160 and 172 > >> can affect > >> > > those rates by up to 10%. So, now people are finding that > this > >> thing > >> > called > >> > > CSA is relatively improtant and should be better understood. > >> > > > >> > > In many analysis techniques, such as relax, you have the > option of > >> > letting > >> > > the CSA vary. For relax, I believe that's models m10-m19 and > >> tm10-tm19. > >> > > One word of warning though, I wouldn't encourage fitting > the CSA > >> unless > >> > you > >> > > have data at multiple field strengths as you're adding another > >> variable to > >> > > the analysis, so the standard 3 measurements at a single field > >> strength > >> > are > >> > > likely not enough to do this. You also run the risk of > >> overinterpretting > >> > > your data because, in my opinion, varying the CSA freely in > >> relaxation > >> > > analysis is not unlike simply throwing in a fudge factor. :-) > >> > > > >> > > As for what is the best value to use, I can't really help you > >> there. > >> > We'll > >> > > have to wait for some of the protein people to respond (I know > >> RNA better > >> > > ;-) ). But if you're at low enough fields or tiny proteins > (<2-3 > >> ns tau( > >> > m > >> > > )) it shouldn't really matter what you use. > >> > > > >> > > I hope all of this makes sense and I haven't said anything > >> blatantly > >> > > incorrect. If I have, hopefully someone will follow up on both > >> of our > >> > > posts. Thanks, and good luck! > >> > > > >> > > Alex Hansen > >> > > > >> > > > >> > > > >> > > > >> > > Hi > >> > > > >> > > I am new to relax and have a quite general question about the > >> value used > >> > > for the CSA while studying proteins' 15N-1H vectors with > model-free > >> > > approach. > >> > > > >> > > In the litterature, we mainly find two values for the CSA > (-160 > >> and -172 > >> > > > >> > > ppm). > >> > > > >> > > There is, if I understand well, a link between the bond length > >> and the > >> > > CSA, but everyone seems to agree about using the same value of > >> 1.02 A > >> > > which should give rise to a mean S2 of 0.85 for secondary > >> structure when > >> > > > >> > > combined to a CSA of -172 ppm. > >> > > > >> > > In the relax sample scripts (as well as in the Model-free > manual), a > >> > > value of -160 ppm is used for CSA. > >> > > > >> > > What is the best value to use and, most importantly, why ? > >> > > > >> > > > >> > > Also, what about the CSA variability from one vector to another > >> (JACS, > >> > > 128 (24), 7855 -7870, 2006) ? > >> > > > >> > > Thanks ! > >> > > > >> > > > >> > > Sébastien > >> > > > >> > > ________________________________ > >> > > > >> > > _______________________________________________ > >> > > relax (http://nmr-relax.com) > >> > > > >> > > This is the relax-users mailing list > >> > > [email protected] <mailto:[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 > >> > > > >> > > > >> > > > >> > > -- > >> > > > >> > > ______________________________________ > >> > > _______________________________________________ > >> > > | | > >> > > || Sebastien Morin || > >> > > ||| Etudiant au doctorat en biochimie ||| > >> > > |||| Laboratoire de resonance magnetique nucleaire |||| > >> > > ||||| Dr Stephane Gagne ||||| > >> > > |||| CREFSIP (Universite Laval) |||| > >> > > ||| 1-418-656-2131 poste 4530 ||| > >> > > || [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> || > >> > > |_______________________________________________| > >> > > ______________________________________ > >> > > > >> > > > >> > > _______________________________________________ > >> > > relax (http://nmr-relax.com) > >> > > > >> > > This is the relax-users mailing list > >> > > [email protected] <mailto:[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 > <https://mail.gna.org/listinfo/relax-users> > >> > > > >> > > > >> > > > >> > > >> > _______________________________________________ > >> > relax (http://nmr-relax.com <http://nmr-relax.com>) > >> > > >> > This is the relax-users mailing list > >> > [email protected] <mailto:[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 > <https://mail.gna.org/listinfo/relax-users> > >> > > >> > > >> > >> > > > > > > -- > ______________________________________ > _______________________________________________ > | | > || Sebastien Morin || > ||| Etudiant au PhD en biochimie ||| > |||| Laboratoire de resonance magnetique nucleaire |||| > ||||| Dr Stephane Gagne ||||| > |||| CREFSIP (Universite Laval, Quebec, CANADA) |||| > ||| 1-418-656-2131 #4530 ||| > || || > |_______________________________________________| > ______________________________________ > > > > > > -- > 4635 Hunt Club Dr Apt 1C > Ypsilanti, MI - 48197 > > Cell: (734) 819-0928 > Work: (734) 615-7421 -- ______________________________________ _______________________________________________ | | || Sebastien Morin || ||| Etudiant au PhD en biochimie ||| |||| Laboratoire de resonance magnetique nucleaire |||| ||||| Dr Stephane Gagne ||||| |||| CREFSIP (Universite Laval, Quebec, CANADA) |||| ||| 1-418-656-2131 #4530 ||| || || |_______________________________________________| ______________________________________
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