Starting a Fit

Command

To fit NMR chemical exchange datasets, use the chemex fit command from the command line. This command accepts various options to customize the fitting process:

chemex fit <options>

Options

The table below lists the available options for chemex fit. Each option links to a detailed explanation, which you’ll find in subsequent sections.

Name	Description
-e or --experiments	Specify files containing experimental setup and data.
-p or --parameters	Specify files containing initial fitting parameters.
-m or --methods	Indicate the fitting method file (optional).
-d or --model	Specify the kinetic model for fitting (optional, default: 2st).
-o or --output	Set the output directory (optional, default: ./Output).
--plot {nothing, normal, all}	Select the plotting level (optional, default: normal).
--include	Define residues to include in the fit (optional).
--exclude	Define residues to exclude from the fit (optional).

note

The --experiments and --parameters options are required.

tip

For options that accept files (e.g., -p), you can use the wildcard character (*) to input multiple files collectively, rather than listing each file individually.

TOML File Formats

ChemEx uses the TOML format for input and output files. For more information about this format, visit the TOML website.

Combining Multiple Experiments

ChemEx supports combined analysis of multiple experiments. To include various experiments in a fit, list the corresponding experiment files after the --experiments (or -e) option. This feature is particularly useful for fitting different types of CEST or CPMG experiments or a combination of both.

For an example of protein-ligand binding analysis using both CPMG and CEST experiments, see this example.

Example

Here is a typical command for running ChemEx:

chemex fit -e Experiments/*.toml \
           -p Parameters/parameters.toml \
           -m Methods/method.toml \
           -o Output

Output files are saved in the directory specified by -o. By default, plots illustrating best-fit lines are generated; you can adjust this behavior with the --plot option.

tip

For convenience, consider saving this command in a shell script, typically named run.sh:

#!/bin/sh

chemex fit -e Experiments/*.toml \
           -p Parameters/parameters.toml \
           -m Methods/method.toml \
           -o Output

To make the script executable, run:

chmod +x run.sh