Additional Modules
Simulating CPMG and CEST Profiles
ChemEx enables the simulation of CPMG or CEST profiles based on a specified set of input parameters. These simulations are useful for exploring the impact of each parameter on the results.
To run a simulation in ChemEx, use the following command:
chemex simulate -e <FILE> \
-p <FILE> \
-d <MODEL> \
-o <DIR>
Example simulation results for CPMG and CEST experiments are shown below:
Options
| Option | Description |
|---|---|
-e, --experiments | Specifies the files containing experimental setup and data location |
-p, --parameters | Specifies the files containing the initial parameter values |
-d, --model | Specifies the exchange model used for simulation (default: 2st) |
-o, --output | Specifies the output directory (default: ./OutputSim) |
--plot {nothing,normal} | Sets the plotting level (default: normal) |
--include | Residues to include in the simulation (optional) |
--exclude | Residues to exclude from the simulation (optional) |
Example
An example script for running simulations can be found here in the simulate.sh file.
Plotting Best-Fit Parameters
The plot_param module in ChemEx allows you to visualize fitting results interactively.
Options
| Option | Description |
|---|---|
-p, --parameters | Specifies the files containing fitted parameters for plotting |
-n, --parname | Specifies the name of the parameter to plot |
Example
An example of using this module is available in the protein-ligand binding example. After running run.sh, display the chemical shift differences between free and bound states with:
chemex plot_param -p Output/STEP2/Parameters/fitted.toml -n DW_AB
To compare the transverse relaxation rates of both states, use:
chemex plot_param -p Output/STEP2/Parameters/fitted.toml -n R2
These commands are also included in the plot_param.sh script in this example. By analyzing these parameters, the core interaction site can be identified, along with a tail at the C-terminal end displaying increased R2 rates and minimal chemical shift changes. This tail may indicate transient interactions with the binding partner, causing steric restrictions in that region.
Initial Estimates of Δϖ for CEST Experiments
In CEST (and D-CEST/COS-CEST) experiments, choosing appropriate initial values
for Δϖ can help avoid local minima. The pick_cest module lets you assign two
dips to the A and B labels and generates initial CS_A and DW_AB values. You
may use a major/ground-state A and minor/excited-state B convention, but the tool
does not establish that physical assignment or enforce a population ordering.
Use the following command to launch the pick_cest module:
chemex pick_cest -e <FILE> -o <DIR>
Upon running this command, a window displaying all CEST profiles appears. For
each profile, click first on the dip to assign to A and then on the dip to assign
to B. If only one dip is visible, click it twice. Use Next and Previous to
navigate profiles, Swap to exchange the A/B assignments, and Clear to reset
the current profile. The tool writes cs_a.toml and dw_ab.toml in real time,
with DW_AB = CS_B - CS_A. These are initialization files; the assignments are
not inferred or validated as major/minor states. See
Exchange States and Parameters for the
state-label and shift-sign conventions.
Example
Scripts to try out this module are provided in the pick_cest.sh file under the CEST_15N example and pick_dcest.sh file under the DCEST_15N example for CEST and D-CEST experiments, respectively.