Matplotlib DPL94 R1rho R2eff

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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

  • Evenäs, J., Malmendal, A. and Akke, M. (2001). Dynamics of the transition between open and closed conformations in a calmodulin C-terminal domain mutant. Structure, 9(3), 185-195. (DOI: 10.1016/S0969-2126(01)00575-5)
  • Kempf, J. G. and Loria, J. P. (2004). Measurement of intermediate exchange phenomena. Methods Mol. Biol., 278, 185-231. (DOI: 10.1385/1-59259-809-9:185)
  • Massi, F., Grey, M. J., Palmer, 3rd, A. G. (2005). Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1ρ relaxation experiments Protein science, 14(3), 735-742. (DOI: 10.1110/ps.041139505)
  • Palmer, 3rd, A. G., Kroenke, C. D., and Loria, J. P. (2001). Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol., 339, 204-238. (DOI: 10.1016/S0076-6879(01)39315-1)
  • Palmer, 3rd, A. G. and Massi, F. (2006). Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev., 106(5), 1700-1719. (DOI: 10.1021/cr0404287)

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

Figure 1
Figure 2
Figure 3

To run

relax -p r1rhor2eff.py

Code

Bugs ?

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

See also