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:
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]]