EM restraints

Precomputed EM fits

The restraints calculated from pre-calculated fit libraries.

They are created automatically if the fit libraries are defined as positions in the JSON configuration file and named discrete_restraints.

If you want to use them, add discrete_restraints to your scoring functions.

Parameters:

discrete_restraints_weight: Weight for restraints derived from the pre-defined positions, e.g. precomputed libraries of fits., default: 1.0

FitRestraint

The standard cross-correlation-based EM restraints implemented using FitRestraint from IMP

It can be defined in the JSON configuration file using blocks like this:

{
    "active": true,
    "type": "em_map",
    "name": "FitRestraint",
    "em_restraint_type": "FitRestraint",
    "filename": "EM_data/emd_4151_binned.mrc",
    "voxel_size": 6.6,
    "resolution": 25,
    "weight": 1000,
    "first_copy_only": false,
    "repr_resolution": 10,
    "optimized_components": [
        {"name": "Elp1", "subunit": "Elp1"},
        {"name": "Elp2", "subunit": "Elp2"},
        {"name": "Elp3", "subunit": "Elp3"}

    ]
}

Parameters

active: true or false, whether the restraint should be created, you can set to false to save on loading time if you don’t need this restraint (even if it’s true, you still need to add it to a scoring function to have it an effect)
type: must be: em_map
name: whatever name. Use this name to refer to this restraint in Parameter file when defining the scoring functions
em_restraint_type: must be: FitRestraint
filename: relative or absolute path to the map in the MRC format
voxel_size: Pixel/voxel size of the map in Angstrom
resolution: Resolution for the EM map simulated from the model for cross-correlation calculation. Can be e.g. approximately the resolution of your map.
weight: Weight of this restraint
first_copy_only: true or false, Apply only to the first molecule copy of each series?
repr_resolution: The resolution of representation to which this restraint should be applied
optimized_components: A list of Selectors defining molecules or parts to which this restraint should be applied to.

EnvelopePenetrationRestraint

A restraint promoting particles to be covered by an EM map envelope at a defined density threshold, implemented using EnvelopePenetrationRestraint from IMP

It can be defined in the JSON configuration file using blocks like this:

{
    "active": true,
    "type": "em_map",
    "name": "Elys_in_difference_density",
    "em_restraint_type": "EnvelopePenetrationRestraint",
    "filename": "EM/map.mrc",
    "threshold": 0.001,
    "voxel_size": 6.9,
    "resolution": 20,
    "weight": 1000,
    "first_copy_only": true,
    "repr_resolution": 10,
    "optimized_components": [
        {
            "name": "Elys",
            "subunit": "Elys"
        }
    ]
}

Parameters

active: true or false, whether the restraint should be created, you can set to false to save on loading time if you don’t need this restraint (even if it’s true, you still need to add it to a scoring function to have it an effect)
type: must be: em_map
name: whatever name. Use this name to refer to this restraint in Parameter file when defining the scoring functions
em_restraint_type: must be: EnvelopePenetrationRestraint
threshold: Density threshold to define the EM envelope
filename: relative or absolute path to the map in the MRC format
voxel_size: Pixel/voxel size of the map in Angstrom
resolution: Resolution for the EM map simulated from the model for cross-correlation calculation. Can be e.g. approximately the resolution of your map.
weight: Weight of this restraint
first_copy_only: true or false, Apply only to the first molecule copy of each series?
repr_resolution: The resolution of representation to which this restraint should be applied
optimized_components: A list of Selectors defining molecules or parts to which this restraint should be applied to.

ExcludeMapRestraint1

A restraint preventing particle penetration of an EM density. Can used for example to prevent penetration of a segmented membrane density or density segment known to be occupied by other subunits.

Yes, the name with 1 at the end ;-)

{
    "active": true,
    "type": "em_map",
    "name": "exclude_membrane",
    "em_restraint_type": "ExcludeMapRestraint1",
    "filename": "../EM/Membrane_final_resampled_no_neg.mrc",
    "threshold": 0.02,
    "voxel_size": 6.9,
    "resolution": 20,
    "weight": 100000,
    "first_copy_only": false,
    "repr_resolution": 10,
    "optimized_components": [
        {
            "name": "Nup120",
            "subunit": "Nup120",
            "copies": [0,1]
        },
        {
            "name": "Nup189c",
            "subunit": "Nup189c",
            "copies": [0,1]
        }
    ]
}

Parameters

active: true or false, whether the restraint should be created, you can set to false to save on loading time if you don’t need this restraint (even if it’s true, you still need to add it to a scoring function to have it an effect)
type: must be: em_map
name: whatever name. Use this name to refer to this restraint in Parameter file when defining the scoring functions
em_restraint_type: must be: ExcludeMapRestraint1
threshold: Density threshold to define the EM envelope
filename: relative or absolute path to the map in the MRC format
voxel_size: Pixel/voxel size of the map in Angstrom
resolution: Resolution for the EM map simulated from the model for cross-correlation calculation. Can be e.g. approximately the resolution of your map.
weight: Weight of this restraint
first_copy_only: true or false, Apply only to the first molecule copy of each series?
repr_resolution: The resolution of representation to which this restraint should be applied
optimized_components: A list of Selectors defining molecules or parts to which this restraint should be applied to.

CloseToEnvelopeRestraint

A restraint pulling particles towards the envelope defined density. The restraint is 0 if the particle is at the envelope defined at the provided threshold and increases with the distance from the envelope, either inside or outside of the envelope.

Can be used for example to restrain membrane binding regions to a membrane.

bring particles into the target EM density where they will be fitted by the other EM restraint.

{
    "active": true,
    "type": "em_map",
    "name": "Nup132_close_to_membrane1",
    "em_restraint_type": "CloseToEnvelopeRestraint",
    "filename": "../EM/Membrane_final_resampled_no_neg.mrc",
    "threshold": 0.02,
    "voxel_size": 6.9,
    "resolution": 20,
    "weight": 2000,
    "max_distance": 200,
    "first_copy_only": false,
    "repr_resolution": 10,
    "optimized_components": [
        {
            "name": "Nup132",
            "subunit": "Nup132",
            "domain": "membrane_binding",
            "copies": [
                0,1
            ],
            "serie": "NR_1"
        }
    ]
}

Parameters

active: true or false, whether the restraint should be created, you can set to false to save on loading time if you don’t need this restraint (even if it’s true, you still need to add it to a scoring function to have it an effect)
type: must be: em_map
name: whatever name. Use this name to refer to this restraint in Parameter file when defining the scoring functions
em_restraint_type: must be: CloseToEnvelopeRestraint
threshold: Density threshold to define the EM envelope
filename: relative or absolute path to the map in the MRC format
voxel_size: Pixel/voxel size of the map in Angstrom
resolution: Resolution for the EM map simulated from the model for cross-correlation calculation. Can be e.g. approximately the resolution of your map.
weight: Weight of this restraint
max_distance: Distance of a particle from the envelope at which to start evaluating the restraint, default 100 A. Increasing may decrease computational speed.
first_copy_only: true or false, Apply only to the first molecule copy of each series?
repr_resolution: The resolution of representation to which this restraint should be applied
optimized_components: A list of Selectors defining molecules or parts to which this restraint should be applied to.

EnvelopeFitRestraint

A restraint from IMP that “fits the particles into the density map by alignment of principal components of the particles with principal components of the map”, read more EnvelopeFitRestraint from IMP

I never use it.

It can be defined in the JSON configuration file using blocks like this:

{
    "active": true,
    "type": "em_map",
    "name": "restraint_type_I_never_use",
    "em_restraint_type": "EnvelopeFitRestraint",
    "filename": "EM/map.mrc",
    "threshold": 0.001,
    "voxel_size": 6.9,
    "resolution": 20,
    "weight": 1000,
    "first_copy_only": true,
    "repr_resolution": 10,
    "optimized_components": [
        {
            "name": "Elys",
            "subunit": "Elys"
        }
    ]
}

Parameters as above for EnvelopePenetrationRestraint.