EM restraints ============= Precomputed EM fits ------------------- The restraints calculated from :doc:`pre-calculated fit libraries`. They are created automatically if the fit libraries are defined as :doc:`positions` in the :doc:`json` 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 :doc:`json` using blocks like this: .. code-block:: json { "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 :doc:`params` 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 :doc:`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 :doc:`json` using blocks like this: .. code-block:: json { "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 :doc:`params` 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 :doc:`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 ;-) .. code-block:: json { "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 :doc:`params` 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 :doc:`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. .. code-block:: json { "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 :doc:`params` 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 :doc:`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 :doc:`json` using blocks like this: .. code-block:: json { "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.