Starting a Fit
Command
To initiate a fit of NMR chemical exchange datasets, use the chemex fit command in the command line. This command can be accompanied by various options to customize the fitting process:
chemex fit <options>
Options
The following table lists the options for chemex fit. Each option's name is a link to its detailed explanation, and these options are further elaborated 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). |
The --experiments and --parameters options are mandatory.
For file-input arguments (e.g., -p), you can use the wildcard character (*) to collectively input multiple files instead of listing each file individually.
ChemEx uses the TOML file format for its input and output files. You can find detailed information about this format on the TOML website.
Combining Multiple Experiments
ChemEx facilitates the combined analysis of multiple experiments. To include various experiments in a fit, add their corresponding experiment files after the --experiments (or -e) option in the command line. This is particularly useful for fitting different types of CEST or CPMG experiments, or a combination thereof.
See an example of protein-ligand binding analysis using both CPMG and CEST experiments here.
Example
A typical command for invoking ChemEx is as follows:
chemex fit -e Experiments/*.toml \
-p Parameters/parameters.toml \
-m Methods/method.toml \
-o Output
The output files are saved in the directory specified by -o. The default setting includes the generation of plots to illustrate the best fit lines, which can be adjusted using the --plot option.
For convenience, consider saving this command in a shell script, commonly named run.sh in examples:
#!/bin/sh
chemex fit -e Experiments/*.toml \
-p Parameters/parameters.toml \
-m Methods/method.toml \
-o Output
To make the script executable, use:
chmod +x run.sh