Parameter Files

Overview

Parameter names use stable state labels and directional conventions. Before preparing values, read Exchange States and Parameters, especially the definitions of PB, KEX_AB, KAB, KBA, and DW_AB.

Parameter files contain initial estimates for the parameters used in the fitting process. These files are specified in ChemEx using the -p or --parameters option:

chemex fit [...] -p <parameter_file> [...]

Parameter files are organized into sections:

• The [GLOBAL] section applies parameters universally to all residues.
• Residue-specific parameters are defined in sections named after each parameter, such as [CS_A]. Multiple parameter files can be provided if needed.

warning

To ensure accurate results and avoid local minima, set appropriate initial values for each parameter, as the χ² minimization process involves multidimensional searching.

info

If no initial value is provided in the parameter files, a default value will be assigned.

Example Parameter File

Below is an example of a parameter file:

parameters.toml

[GLOBAL]
PB     = 0.015
KEX_AB = 70.0
TAUC_A = 10.0

[CS_A]
13N = 108.207
26N = 115.711
28N = 113.882
29N = 115.318
33N = 115.636
37N = 116.159
41N = 114.635
42N = 113.525
43N = 108.876
50N = 107.855
52N = 111.358
55N = 128.301
59N = 116.388
66N = 119.429
67N = 114.454
68N = 120.595

[DW_AB]
13N = 4.0
26N = 5.5
28N = 6.5
29N = 6.0
33N = 4.5
37N = 5.0
41N = 6.0
42N = 6.0
43N = 12.5
50N = 8.0
52N = 8.5
55N = -6.5
59N = 6.5
66N = 4.0
67N = 8.0
68N = 4.5

tip

Setting model-free parameters (e.g., TAUC_A) can provide a good initial estimate for relaxation parameters (e.g., R1_A, R2_A). For biomolecules in H₂O at T = 300 K, the overall tumbling time is roughly 1 ns per 2.6 kDa of molecular weight. Tumbling time is proportional to η/T, where η is solution viscosity and T is temperature in Kelvin.

Setting Parameter Bounds

To set upper and lower bounds for any fitting parameter, replace the initial value with a list of three elements:

parameters.toml

PARAMETER_WITH_NO_BOUNDS = <initial_value>
PARAMETER_WITH_BOUNDS = [<initial_value>, <lower_bound>, <upper_bound>]

Standard independent ChemEx parameters have finite default safety bounds. A scalar parameter-file value changes only the initial value and inherits that standard domain. The three-element form replaces both default bounds for the matching parameter, so explicit parameter-file bounds retain precedence.

These broad domains protect deterministic fitting from unrealistic regions; they are not intended as informative scientific priors. They are also the support of the uniform distribution used by current MCMC. Before running MCMC, inspect the effective bounds and override them when scientific prior knowledge requires a different domain. In particular, the model-free order parameter S2 is restricted to its physical [0, 1] domain by default.

Avoid overly strict bounds, because they can hinder convergence. The supported trf fit method honors the effective finite bounds.