Additional modules

Simulating CPMG and CEST profiles

ChemEx allows simulating CPMG or CEST profiles based on a given set of input parameters. Such simulations may be useful to learn about the effects of each individual parameter on the final results.

A typical command for simulation purposes with ChemEx is like this:

   chemex simulate -e <FILE> \
                   -p <FILE> \
                   -d <MODEL> \
                   -o <DIR>

Example simulation results for CPMG and CEST experiments are shown below:

Examples of CEST and CPMG simulation results

Options

Option	Description
-e, --experiments	Specify the files containing experimental setup and data location
-p, --parameters	Specify the files containing the initial values of fitting parameters
-d, --model	Specify the exchange model used to fit the datasets (default: 2st)
-o, --output	Specify the output directory (default: ./Output)
--plot {nothing,normal}	Plotting level (default: normal)
--include	Residue(s) to include in the fit (optional)
--exclude	Residue(s) to exclude from the fit (optional)

Example

An example use of the module is available here with the script simulate.sh.

Plotting best-fit parameters

ChemEx comes with a module plot_param that allows visualizing the fitting results interactively.

Options

Option	Description
-p, --parameters	Specify the files containing the fitted parameters to be plotted
-n, --parname	Specify the name of the parameter to plot

Example

An example use of the module is given in the protein-ligand binding example. After finish running run.sh, the chemical shift differences between the free and bound states can be displayed with:

chemex plot_param -p Output/STEP2/All/Parameters/fitted.toml -n DW_AB

and the transverse relaxation rates of both states can be compared with:

chemex plot_param -p Output/STEP2/All/Parameters/fitted.toml -n R2

These two commands are saved in the plot_param.sh script in this example. From these two observables, the core region of the interaction site can be clearly located. Aside from the core region, there is also a tail with increased R₂ rates located at C-terminal end of the interaction site and with very little chemical shift perturbation. This region is likely involved in the transient interactions with the binding partner, which causes certain degree of steric restriction to this region.

Getting initial estimates of Δϖ for CEST experiments

In CEST (and also D-CEST/COS-CEST) experiments, it is necessary to choose suitable initial value of Δϖ to avoid getting trapped in a local minimum. ChemEx comes with a module pick_cest for manually picking the major and minor dips of CEST profiles, which correspond to the ground and excited states, respectively. A typical command for such purpose is like this:

chemex pick_cest -e <FILE> -o <DIR>

After typing this command, a window showing all CEST profiles will appear. For each profile first click on the major dip and then on the minor dip(s). Note that in certain profiles only one dip could be visible, which indicates the minor dip is overlapped with the major dip, therefore the major dip should be clicked twice. When done with any profile, click the Next or Previous button to proceed to the next or previous profile. The Swap button allows switching between the major and minor states. The Clear button allows cleaning the selection in the current profile. Two separate files will be created in real-time during the dip picking process: cs_a.toml and dw_ab.toml that contain chemical shifts of the major state and chemical shift difference between the major and minor states, respectively.

Example

Try to run the pick_cest.sh script under CEST_15N/ example and pick_dcest.sh script under DCEST_15N/ example to learn how to make use of this function for CEST and D-CEST experiments, respectively.