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DPL94

306 bytes added, 15:01, 18 November 2015
→‎Parameter name space in relax: Included a number of code tags.
= Intro =
The Davis et al., 1994 2-site off-resonance fast exchange relaxation dispersion model for [[R1rho-type data]]. It extends the [[M61]] model to off-resonance data, hence it collapses to this model for on-resonance data. The model is labelled as '''DPL94''' in [[Relaxation dispersion citation for relax|relax]].
== Parameters ==
The DPL94 model has the parameters {$R_{1\rho{:R1rhoprime}}'$, $...$, $\Phi_{ex{:Phiex}}$, $k_{ex{:kex}}$}.
=== Essentials === {{note|{{:R1}} should be provided in rad/s, the SI default unit for this relaxation rate.}} It is essential to read in $R_{1{:R1}}$ values before starting a calculation:<br>Note, R1 should be provided in rad/s.
<source lang="python">
relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_values.txt', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
== Parameter name space in relax ==
 {{collapsible script| type = relax script| title = At time of writing (March 2014) the parameters in relax was were stored as:demonstrated in this script.<source | lang ="python">| script =
# Load the outcome from an analysis
state.load(state="results.bz2", dir="results/final")
else:
print(mol_name, res_num, res_name, spin_id, curspin.r2, curspin.phi_ex, curspin.kex)
}}
<[http:/source>/www.nmr-relax.com/manual/Dispersion_model_summary.html Please see the summary of the model parameters here.]
Which means:
# $R_{1\rho{:R1rhoprime}}'$ = <code>spin.r2 </code> (Fitted)# $R_{1\rho{:R1rho}}$ = <code>spin.r2eff </code> (Back calculated)# $\Phi_{ex{:Phiex}}$ = <code>spin.phi_ex </code> (Fitted)# $k_{ex{:kex}}$ = <code>spin.kex </code> (Fitted)# $R_{1{:R1}}$ = <code>spin.ri_data['R1'] </code> (Loaded)
Please also see this thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5164
=== Equation - re-writed written forms ===
Discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5207
* {{# Evenäs, J., Malmendal, A. & Akke, M. (2001). Dynamics of the transition between open and closed conformations in a calmodulin C-terminal domain mutant. Structure 9, 185–195 httplst://dx.doi.org/10.1016/S0969-2126(01)00575-5Citations|Evenäs01}}* {{# Kempf, J.G. & Loria, J.P. (2004). Measurement of intermediate exchange phenomena. Methods Mol. Biol. 278, 185–231 httplst://dx.doi.org/10.1385/1-59259-809-9Citations|KempfLoria04}}* {{#lst:185Citations|Massi05}}* {{# Palmer, A.G. & Massi, F. (2006). Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700–1719 httplst://dx.doi.org/10.1021/cr0404287Citations|Palmer01}}* {{# Palmer, A.G., Kroenke, C.D. & Loria, J.P. (2001). Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Meth. Enzymol. 339 httplst://dx.doi.org/10.1016/S0076-6879(01)39315-1Citations|PalmerMassi06}}* {{# Francesca Massi, Michael J. Grey, Arthur G. Palmer III* (2005). Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1ρ relaxation experiments, Protein science httplst://dx.doi.org/10.1110/ps.041139505Citations|TrottPalmer02}}
Different graphs.
==== The {{:R1rho}}: {{: R2 }} or {{:R2eff }} as function of effective field in rotating frame: w_eff {{:omegaeff}} == === Discussion ===It is clear that there is no real name for the pseudo-parameter. It looks like that {{:Reff}} was Art's original way of denoting this and that he has now changed to {{:R2}} instead. <br>But if one look at the reference for the [[TP02|TP02 dispersion model]], one will see yet another notation: Here {{:R2}} does not contain the {{:Rex}} contribution. Also, {{:Reff}} is absent of {{:Rex}}. <br>But in Art's Protein Science paper (Ref [5]), the definition {{:R2}} = {{:R2zero}} + {{:Rex}} is used. The [[MP05|MP05 model reference]] also does not use {{:Reff}}. The {{:Reff}} parameter name is confusing and it seems to have been dropped from 2005 onwards. The {{:Reff}} name appears to be specific to Art Palmer's group and as he himself has dropped it, then it would be best to avoid it too.  Ref [2], Equation 27. Here the calculated value is noted as: R_eff: <math>R_{\text{eff}} = R^{0}_2 + R_{ex} = R_{1\rho}' + R_{ex} = R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\theta)</math> <br>Ref [3], Equation 20. Figure 11+16, would be the reference. Here the calculated value is noted as: R_2: <math>R_{2} = R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\theta)</math>. <br>Ref [4], Equation 43. <math>R_{\text{eff}} = R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\theta)</math> <br>Ref [5], Material and Methods, page 740. Figure 4 would be the wished graphs. Here the calculated value is noted as: R_2: <math>R_{2} = R^{0}_2 + R_{ex}</math>
Ref [2]The following suggestions for the definition of the pseudo-parameters, which can be extracted, Equation 27. Here the calculated value is noted asthen: R_eff: $R_{\text{eff}} <math>R_2 = R^{0}_2 + R_{ex} = R_{1\rho}' + R_{ex} = R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\theta)$ <br>Ref [3], Equation 20. Figure 11+16, would be the reference. Here the calculated value is noted as: R_2: $R_{2} = R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\theta)$. <br>Ref [4], Equation 43. $R_frac{\text{eff}} = R_{1\rho} / \sin^2(\theta) - R_1 / \tancos^2(\theta)$ <br>Ref [5], Material and Methods, page 740. Figure 4 would be the wished graphs. Here the calculated value is noted as: R_2: $R_{2} = R^{0}_2 + R_{ex}$# $R_2 = R^{0}_2 + R_{ex} = R_{1\rho}' + R_{ex} = R_{1\rho} / \sin^2(\theta) - R_1 }</ \tan^2(\theta)$math>
== Reference ==
The reference for the DPL94 model is:
* Davis, D., Perlman, M., and London, R. (1994). Direct measurements of the dissociation-rate constant for inhibitor-enzyme complexes via the T1rho and T2 (CPMG) methods. ''J. Magn. Reson.'', '''104'''(3), 266–275. ([http{{#lst://dx.doi.org/10.1006/jmrb.1994.1084 10.1006/jmrb.1994.1084])Citations|Davis94}}
== Related models ==
The [[Relaxation dispersion citation for relax|implementation of the DPL94 model in relax]] can be seen in the:
* [http://www.nmr-relax.com/manual/DPL94_2_site_fast_exchange_R1_modelThe_DPL94_2_site_fast_exchange_R1_rho_model.html relax manual],
* [http://www.nmr-relax.com/api/3.1/lib.dispersion.dpl94-module.html API documentation],
* [http://www.nmr-relax.com/analyses/relaxation_dispersion.html#DPL94 relaxation dispersion page of the relax website].
== See also ==
[[Category:Relaxation_dispersionModels]][[Category:Dispersion models]][[Category:Relaxation dispersion analysis]]
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