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Matplotlib DPL94 R1rho R2eff

Revision as of 14:26, 3 November 2015 by Bugman (talk | contribs) (→‎Figures: Switched to parameter templates and cleaned up the maths.)

About

The production to these figures relates to the Suppport Request:
sr #3124: Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff

References

Refer to the manual for parameter explanation

  1. 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 DOI
  2. Kempf, J.G. & Loria, J.P. (2004). Measurement of intermediate exchange phenomena. Methods Mol. Biol. 278, 185–231 DOI
  3. Palmer, A.G. & Massi, F. (2006). Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700–1719 DOI
  4. 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 DOI
  5. 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 DOI

Figures

Ref [1], Figure 1.b. The bell-curves As function of angle calculation.

Ref [1], Figure 1.c. The wanted graph. No clear "name" for the calculated parameter.

Ref [2], Equation 27. Here the calculated value is noted as: Reff = R / sin2(θ) - R1 / tan2(θ) = R20 + Rex, where R20 refers to R' as seen at DPL94

Ref [3], Equation 20. Here the calculated value is noted as: R2 = R / sin2(θ) - R1 / tan2(θ). Figure 11+16, would be the reference.

Ref [4], Equation 43. Reff = R / sin2(θ) - R1 / tan2(θ).

Ref [5], Material and Methods, page 740. Here the calculated value is noted as: R2: R2 = R20 + Rex. Figure 4 would be the wished graphs.


A little table of conversion then gives

Relax equation    |   Relax store    | Articles
---------------------------------------------------------------
R1rho'                spin.r2             R^{0}_2 or Bar{R}_2
Fitted pars           Not stored          R_ex
R1rho                 spin.r2eff          R1rho
R_1                   spin.ri_data['R1']  R_1 or Bar{R}_1

The parameter is called R_2 or R_eff in the articles. Since reff is not used in relax, this could be used?

A description could be:

  • The effective rate
  • The effective transverse relaxation rate constant
  • The effective relaxation rate constant.

Make graphs

The outcome

To run

relax -p r1rhor2eff.py

Code

Bugs ?

Do you get an error with matplotlib about dateutil? Then see Matplotlib_dateutil_bug

See also