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ChemEx

website·Indexed 30 days ago

https://gbouvignies.github.io/ChemEx/

A command-line tool for analyzing NMR chemical exchange datasets. ChemEx provides capabilities for fitting data using various kinetic models, including N-state and Eyring models, and supports the simulation of CPMG and CEST profiles. The software includes specialized modules for experiments such as CPMG, CEST, and relaxation, and supports multicore execution for its statistics phase.

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What's inside ChemEx

  1. Overview of the cpmg_ch3_13c_h2c_0013 module

    The cpmg_ch3_13c_h2c_0013 module measures methyl carbon chemical exchange in site-specifically 13CH3-labeled proteins within a highly deuterated background. It uses a [0013] phase cycle for CPMG pulses and incorporates purge gradients around the P-element to reduce off-resonance effects, pulse miscalibration, and variations in 1JCH coupling constants. The module supports both even and odd values for ncyc (where odd values result in unequal CPMG pulse counts on either side of the P-element).

  2. Overview of the cpmg_ch3_13c_h2c module

    The cpmg_ch3_13c_h2c module measures methyl carbon chemical exchange for site-specifically 13CH3-labeled proteins in a highly deuterated background. Magnetization starts as anti-phase and is read out as in-phase. Due to the P-element, only even ncyc should be recorded. The resulting magnetization intensity is calculated using a (6n)×(6n) two-spin matrix.

  3. Overview of ChemEx for NMR chemical exchange analysis

    ChemEx is an open-source Python application used to analyze NMR chemical exchange data (such as CPMG, R1ρ, and CEST experiments). It extracts kinetic parameters (rates), thermodynamic parameters (populations), and structural information (chemical shifts) of sparsely populated excited states. Unlike tools relying on analytical equations, ChemEx integrates the evolution matrix of the spin system over the pulse sequence, allowing it to simulate complex kinetic models (e.g., 3-state exchange) and various experimental types (e.g., D-CEST/COS-CEST) while accounting for finite pulse width and off-resonance effects.

  4. Overview of the cpmg_ch3_1h_tq module

    The cpmg_ch3_1h_tq module measures methyl proton chemical exchange for site-specifically 13CH3-labeled proteins in a highly deuterated background. It records magnetization that is initially anti-phase and read out as anti-phase. The calculation utilizes a simplified scheme with a (6n)×(6n) basis set and a two-spin matrix, where n is the number of states.

  5. Overview of ChemEx for NMR chemical exchange analysis

    ChemEx is an open-source Python application used to analyze NMR chemical exchange data (such as CPMG, R1ρ, and CEST experiments). It extracts kinetic parameters (rates), thermodynamic parameters (populations), and structural information (chemical shifts) of sparsely populated excited states. Unlike tools relying on analytical equations, ChemEx integrates the evolution matrix of the spin system over the pulse sequence, allowing it to simulate virtually any kinetic model (e.g., 3-state exchange) or experiment type (e.g., D-CEST/COS-CEST) while accounting for experimental details like finite pulse width and off-resonance effects.

    Key features include:

    • Multi-step fits and joint analysis of datasets from different experiments.
    • Error analysis and grid search.
    • Deterministic fitting using bounded SciPy trust-region reflective least squares.
    • Implementation via NumPy, SciPy, Matplotlib, Rich, and pydantic.

  6. Overview of the dcest_13c module

    The dcest_13c module analyzes chemical exchange in the presence of ¹H composite decoupling during the D-CEST block. This approach ensures the spin system remains purely in-phase throughout the process. Calculations are performed using a (3n)×(3n) single-spin matrix, where n represents the number of states (e.g., { Ix(a), Iy(a), Iz(a), Ix(b), Iy(b), Iz(b), ... }).

  7. Overview of the cest_15n_tr module

    The cest_15n_tr module is used to analyze chemical exchange during the CEST block. It calculates magnetization evolution using a (6n)×(6n) two-spin matrix, where n represents the number of states. This implementation is based on the method described by D. Long, G. Bouvignies, and L.E. Kay in Proc. Natl. Acad. Sci. USA 111, 8820-8825 (2014).

  8. Overview of exchange-induced chemical shift experiments in ChemEx

    ChemEx provides a suite of experiments for analyzing exchange-induced chemical shifts. A primary available experiment is the ¹⁵N exchange induced shifts using ¹⁵N–¹H HSQC/HMQC (identified as shift_15n_sqmq).

  9. Overview of the cpmg_chd2_1h_ap module

    The cpmg_chd2_1h_ap module measures methyl proton chemical exchange recorded on site-specifically 13CHD2-labeled proteins in a highly deuterated background. It handles magnetization that is initially anti-phase and read out as anti-phase prior to 13C evolution. The resulting magnetization intensity after the CPMG block is calculated using a (6n)×(6n) two-spin matrix, where n is the number of states.

  10. Overview of the cpmg_ch3_1h_tq module

    The cpmg_ch3_1h_tq module measures methyl proton chemical exchange recorded on site-specifically 13CH3-labeled proteins in a highly deuterated background. Magnetization is initially anti-phase and is read out as anti-phase. The calculation utilizes a simplified scheme with a (6n)×(6n) basis set and a two-spin matrix, where n is the number of states.

  11. Overview of the cpmg_ch3_1h_dq module

    The cpmg_ch3_1h_dq module is used to measure methyl proton chemical exchange recorded on site-specifically 13CH3-labeled proteins in a highly deuterated background. Magnetization is initially anti-phase and read out as anti-phase. The calculation employs a simplified scheme using a two-spin matrix with a (6n)×(6n) basis set, where n is the number of states.

  12. Overview of the dcest_13c module

    The dcest_13c module analyzes chemical exchange in the presence of ¹H composite decoupling during the D-CEST block. This approach keeps the spin system purely in-phase throughout the process. Calculations are performed using a (3n)×(3n) single-spin matrix, where n represents the number of states (e.g., { Ix(a), Iy(a), Iz(a), Ix(b), Iy(b), Iz(b), ... }).