Changes

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]].

\mathrm{R}_{1\rho}= \mathrm{R}_1\cos^2\theta + \left( \mathrm{R}_{1\rho}{´} + \frac{\Phi_\textrm{ex} \textrm{k}_\textrm{ex}}{\`textrm{k}_\textrm{ex}^2 + \omega_\textrm{e}^2} \right)\sin^2\theta

The DPL94 model has the parameters {${{:R1rhoprime}}, ..., {{:Phiex}}, {{:kex}}}. == Essentials == {{note|{{:R1}} should be provided in rad/s, the SI default unit for this relaxation rate.}} It is essential to read in {{:R1}} values before starting a calculation:<br><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)</source> Where the data could be stored like<source lang="text"># mol_name res_num res_name spin_num spin_name value error None 13 L None N 1.323940 0.146870None 15 R None N 1.344280 0.140560None 16 T None N 1.715140 0.136510</source> == Parameter name space in relax == {{collapsible script| type = relax script| title = At time of writing (March 2014) the parameters in relax were stored as demonstrated in this script.| lang = python| script =# Load the outcome from an analysisstate.load(state="results.bz2", dir="results/final") # import spin functionsfrom pipe_control.mol_res_spin import return_spin, spin_loop # Alias one spins13 = return_spin(":13@N") # See attributesdir(s13) # See parametersprint(s13.params)['r2', 'phi_ex', 'kex'] # Print parametersprint(s13.r2){'R1rho - 799.77739910 MHz': xx.yy}print(s13.phi_ex)print(s13.kex) # See Ri data (ri_type: The relaxation data type, i.e. 'R1', 'R2', 'NOE', or 'R2eff'. )print(s13.ri_data){'R1': 1.3239399999999999} # Print all spin idfor curspin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=False): if curspin.select == False: print(mol_name, res_num, res_name, spin_id) else: print(mol_name, res_num, res_name, spin_id, curspin.r2, curspin.phi_ex, curspin.kex)}} [http://www.nmr-relax.com/manual/Dispersion_model_summary.html Please see the summary of the model parameters here.] Which means:# {{:R1rhoprime}} = <code>spin.r2</code> (Fitted)# {{:R1rho}} = <code>spin.r2eff</code> (Back calculated)# {{:Phiex}} = <code>spin.phi_ex</code> (Fitted)# {{:kex}} = <code>spin.kex</code> (Fitted)# {{: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-written forms ==Discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5207 * {{#lst:Citations|Evenäs01}}* {{#lst:Citations|KempfLoria04}}* {{#lst:Citations|Massi05}}* {{#lst:Citations|Palmer01}}* {{#lst:Citations|PalmerMassi06}}* {{#lst:Citations|TrottPalmer02}} Different graphs. == The {{:R1rho}}: {{:R2}} or {{:R2eff}} as function of effective field in rotating frame: {{: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], $Equation 43. <math>R_{\text{eff}} = R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\Phi_theta)</math> <br>Ref [5], Material and Methods, page 740. Figure 4 would be the wished graphs. Here the calculated value is noted as: R_2: <math>R_{2} = R^{0}_2 + R_{ex}$</math> The following suggestions for the definition of the pseudo-parameters, which can be extracted, $k_is then: <math>R_2 = R^{0}_2 + R_{ex} = R_{1\rho}' + R_{ex}$= R_{1\rho} / \sin^2(\theta) - R_1 / \tan^2(\theta) = \frac{R_{1\rho} - R_1\cos^2(\theta)}{\sin^2(\theta)}.</math>

* 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}}

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],

[[Category:Relaxation_dispersionModels]][[Category:Dispersion models]][[Category:Relaxation dispersion analysis]]