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