Hi, Sorry about the late reply, I've been flat out again lately and didn't have a chance to properly review the patches. It did give me time to think about the changes though. Gary's comment about the "central constant for the default CSA" at https://mail.gna.org/public/relax-devel/2007-07/msg00061.html is taken into account in the 1.3 line. However I think that to make this change in the 1.2 line would potentially be too disruptive. Therefore I have applied both patches as attached to your email Seb because I think this is the best way to solve the problem for 1.3 and not being too large a change for 1.2.
Cheers, Edward On 7/22/07, Sébastien Morin <[EMAIL PROTECTED]> wrote: > Hi, > > I've add the relax-devel mailing list on this talk since most of the subject > is > now related to relax design... > > I've tried to solve this issue both in the 1.2 and 1.3 lines. > > > For the 1.2 line : > > It seems we can modify the code by changing every appearance of CSA with a > -170 > ppm value to a -172 ppm value. However, this breaks the test-suite. In fact, > the jw_mapping test breaks with this change but not the model-free test (the > change in parameters must be too small to be detected by the test-suite. Thus, > the test-suite values must be changed to account for the switch in CSA value. > In the patch below, I only corrected the broken test (jw_mapping) but not the > model-free test which is also affected (even if we don't see it). If these > changes are right for solving this issue, the patch > 'patch__default_csa__l1.2_r3351' (see below for the commit log) should be > used. > > The patch 'patch__default_csa__l1.2_r3351' makes uniform the use of the CSA > value (now -172 ppm everywhere) and fixes the test-suite (in jw_mapping) to > account for this change. > > > For the 1.3 line : > > I've added two constants (N15_CSA and NH_BOND_LENGTH) in the > 'physical_constants.py' file. Then, I'v imported these constants in the files > 'test_suite/system_tests/jw_mapping.py', > 'test_suite/system_tests/model_free.py' and 'specific_fns/jw_mapping.py'. I've > also modified some comments so the -172 ppm value for CSA is now the default. > Finally, as the results from calculations using the CSA value will be changed, > I've also modified the test-suite for jw_mapping, but left unchanged other > parts of the test-suite as the changes in CSA value may not affect these (see > above the discussion for the 1.2 line). If these changes are right, the patch > 'patch__default_csa_r__l1.3_r3351' should be used along with its commit log > (see below). > > The patch 'patch__default_csa_r__l1.3_r3351' makes uniform the use of the CSA > value (now -172 ppm everywhere) and fixes the test-suite (in jw_mapping) to > account for this change. It also adds two constants for the CSA and NH bond > length default values. > > > Cheers > > > Séb :) > > > > > Selon Edward d'Auvergne <[EMAIL PROTECTED]>, 22.07.2007: > > > Hi, > > > > I've had a look at both the 1.2 and 1.3 relax lines and have noticed > > that the sample scripts all use the value of -172 ppm whereas > > everywhere in the relax code base the value of -170 ppm is used as the > > default. Although the change won't make much of a difference in the > > final results, for consistency within relax we could have everything > > changed to -172 ppm. It's up to the authors to report the CSA value > > they have used in their manuscripts (something which should be > > considered essential for comparison). > > > > The idea of defining the CSA and bond length in a separate file in the > > 1.3 line is good. There is the file 'physical_constants.py' in the > > base directory just for this and you just import the constants you > > need. They may need distinctive names though (like CSA_VAL, > > BOND_LENGTH, etc.) to avoid problems with the user supplied values in > > the code. > > > > Cheers, > > > > Edward > > > > > > On 7/19/07, Sebastien Morin <[EMAIL PROTECTED]> wrote: > > > > > > 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]> 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]> 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]>: > > > > >> > > > > >> > 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]> 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] > > > > >> > > > > > > >> > > 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] || > > > > >> > > |_______________________________________________| > > > > >> > > ______________________________________ > > > > >> > > > > > > >> > > > > > > >> > > _______________________________________________ > > > > >> > > relax (http://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://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 > > > > >> > > > > > >> > > > > > >> > > > > >> > > > > > > > > > > > > > > > > > > -- > > > > ______________________________________ > > > > _______________________________________________ > > > > | | > > > > || 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 ||| > > > || || > > > |_______________________________________________| > > > ______________________________________ > > > > > > > > > > > > > > ------------------------ > Sébastien Morin > Étudiant M.Sc. 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