Crosslink restraints

Crosslink restraints restrain distance between crosslinked residues.

Loading crosslink data

Follow the guideline in JSON configuration file of how to add crosslinks using the graphical interface of Xlink Analyzer.

Defining the restraints

Crosslinks restraints are defined in the Parameter file by adding blocks like this:

add_xlink_restraints = True
x_min_ld_score = 25
x_weight = 100.0
x_xlink_distance = 30
x_xlink_score_type='HarmonicUpperBound'

and then adding xlink_restraints to scoring_functions (see Parameter file).

If multiple representation resolutions are defined, the crosslinks will be added to the highest resolution possible (the smallest beads).

Parameters

x_xlink_score_type

A type of crosslink restraint.

Options:

‘HarmonicUpperBound’ - 0 below x_xlink_distance, harmonic above, distance calculated between centers of the beads

‘HarmonicUpperBoundSphereDistancePairScore’ - 0 below x_xlink_distance, harmonic above, distance calculated between surfaces of the beads

‘XlinkScore’ - 0 below x_xlink_distance, 1 above

‘LogHarmonic’ - A log harmonic potential with the maximum at x_xlink_distance

‘CombinedHarmonic’: - harmonic above distance of 35 A and log harmonic with the maximum at x_xlink_distance below 35 A

default: HarmonicUpperBound

x_min_ld_score

Only crosslinks with the confidence score above this threshold will be used as restraints. The score must be defined in “score” column of crosslink CSV files (see also Xlink Analyzer documentation), default: 30.0

x_weight

Weight of crosslink restraints, default: 1.0

x_xlink_distance

Target or maximual crosslink distance (depending on the implementation), default: 30.0

x_k

Spring constant for the harmonic potential, default: 1.0

x_inter_xlink_scale

Multiply the weight of inter-molecule crosslinks by this value, default: 1.0

x_first_copy_only

Apply crosslinks only to the first molecule copy of each series, default: False

x_skip_pair_fn

A Python function to skip specific crosslinks. Arguments: p1, p2, component1, component2, xlink Return True to skip the crosslink, default: None

x_log_filename

Optional log file name for printing more information about added and skipped crosslinks, default: None

x_score_weighting

Scale crosslink weights by their score, default: False

xlink_reweight_fn

A custom Python function to scale crosslink weights. Arguments: xlink, weight Return final weight (float), default: None

x_random_sample_fraction

Take this random fraction of crosslinks for modeling, default: 1.0