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Methyl ¹³C–¹H multiple-quantum CPMG

Module name​

"cpmg_ch3_mq"

Description​

Analyzes HyCx methyl group multiple quantum CPMG measured on site-specific 13CH3-labeled methyl groups in a highly deuterated background. Resulting magnetization intensity after the CPMG block is calculated using the (4n)×(4n), two-spin matrix, where n is the number of states:

{ HxCx(a), HyCx(a), HxCy(a), HyCy(a), HxCx(b), HyCx(b), HxCy(b), HyCy(b), ... }

This is a simplified basis set, which assumes ¹³C is on-resonance (i.e., off-resonance effects are not taken into account).

This calculation is designed specifically to analyze data from the experiment found in the reference and can be run with either small_protein_flag = "y" or "n".

Reference​

  • D.M. Korzhnev, K. Kloiber, V. Kanelis, V. Tugarinov and L.E. Kay J. Am. Chem. Soc. 126, 3964-3973 (2004)

Example​

An example use of the module is given here.

Sample configuration file​

experiment.toml
## This is a sample configuration file for the module 'cpmg_ch3_mq'

[experiment]

## Name of the chemex module corresponding to the experiment
name = "cpmg_ch3_mq"

## CPMG relaxation delay, in seconds
time_t2 = 0.02

## Perform the calculation with the purge element [optional, default: false])
# small_protein = false

## Initial condition: equilibrium (all states populated according to their
## equilibrium populations). Set to true for non-equilibrium initial condition
## if chemical shift evolution occurs before the CPMG element in your pulse
## sequence (see Yuwen et al., J. Biomol. NMR 2016, 65:143-156).
## [optional, default: false]
# cs_evolution_prior = false

## State of the observed resonance [optional, default: "a"]
# observed_state = "a"

[conditions]

## 1H Larmor frequency, in MHz
h_larmor_frq = 800.0

## Sample temperature, in Celsius [optional, depending on the kinetic model]
# temperature = 25.0

## Protein concentration, in M [optional, depending on the kinetic model]
# p_total = 500.0e-6

## Ligand concentration, in M [optional, depending on the kinetic model]
# l_total = 50.0e-6

[data]

## Directory containing the profiles [optional, default: "./"]
# path = "./"

## Option defining how intensity uncertainties are estimated.
## "file": uncertainties are taken from the profile files
## "duplicates": uncertainties are calculated from the duplicate points
## [optional, default: "file"]
# error = "file"

  ## List of the profile names and their associated filenames.
  ## The name of the spin systems should follow the Sparky-NMR
  ## conventions.
  [data.profiles]
  L3CD1-HD1  = "L3CD1-QD1.out"
  L3CD2-HD2  = "L3CD2-QD2.out"
  I12CD1-HD1 = "I12CD1-QD1.out"
  V25CG1-HG1 = "V25CG1-QG1.out"
  V25CG2-HG2 = "V25CG2-QG2.out"
  M36CE-HE   = "M36CE-QE.out"