Trusted, Bureaucrats
4,223
edits
Changes
→Parameter name space in relax: Included a number of code tags.
The DPL94 model has the parameters {{{:R1rhoprime}}, ..., {{:Phiex}}, {{:kex}}}.
{{note|{{:R1}} should be provided in rad/s, the SI default unit for this relaxation rate.}}
== 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://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
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 http://dx.doi.org/10.1385/1-59259-809-9lst:185Citations|KempfLoria04}}* {{# 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|Massi05}}* {{# 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|Palmer01}}* {{# 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|PalmerMassi06}}* {{# Trott, O. and Palmer, 3rd, A. G. (2002). R1rho relaxation outside of the fast-exchange limit. J. Magn. Reson., 154(1), 157–160. (httplst://dx.doi.org/10.1006/jmre.2001.2466).Citations|TrottPalmer02}}
Different graphs.
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}} = {{:Rzero2R2zero}} + {{: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.
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 ==
== See also ==
[[Category:Relaxation_dispersion Models]][[Category:Dispersion models]][[Category:Relaxation dispersion analysis]]