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IMP Reference Guide  develop.2640aaee5c,2019/11/13
The Integrative Modeling Platform
IMP::multifit Namespace Reference

Fitting atomic structures into a cryo-electron microscopy density map. More...

Detailed Description

Fitting atomic structures into a cryo-electron microscopy density map.

MultiFit is a computational method for simultaneously fitting atomic structures of components into their assembly density map at resolutions as low as 25Å. The component positions and orientations are optimized with respect to a scoring function that includes the quality-of-fit of components in the map, the protrusion of components from the map envelope, as well as the shape complementarity between pairs of components. The scoring function is optimized by an exact inference optimizer DOMINO that efficiently finds the global minimum in a discrete sampling space.

For more information please see the MultiFit website.

See the IMP::cnmultifit module for a similar protocol for handling symmetric complexes.

multifit: command line tool

Generally, this module is not used directly; instead, the multifit command line tool is used. For an example, see Modeling of 3sfd.

Web server

A webserver that uses both this module and the IMP::cnmultifit module is also available.

complex_to_anchor_graph

Build an anchor graph from a PDB file.

Info

Author(s): Keren Lasker

Maintainer: benmwebb

License: GPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

Classes

class  AnchorsData
 Storage of anchors (points and edges) More...
 
class  AssemblyHeader
 Holds data about the assembly density needed for optimization. More...
 
class  ComplementarityRestraint
 Compute the complementarity between two molecules. More...
 
class  ComponentHeader
 Holds data about a component needed for optimization. More...
 
class  DataPointsAssignment
 
class  DensityDataPoints
 Stores density voxels as a vector of Array1D. More...
 
class  DummyRestraint
 A simple Restraint that always returns a score of zero. More...
 
class  Ensemble
 An ensemble of fitting solutions. More...
 
class  FFTFitting
 Fit a molecule inside its density by local or global FFT. More...
 
class  FFTFittingOutput
 Storage of the results from an FFT fit. More...
 
class  FittingSolutionRecord
 A fitting solution record. More...
 
class  FittingStates
 
class  GeometricHash
 Geometric Hash table. More...
 
class  MergeTreeBuilder
 Utility class for building merge trees. More...
 
class  ProbabilisticAnchorGraph
 Probabilistic anchor graph. More...
 
class  ProteinsAnchorsSamplingSpace
 stores the anchors sampling space for each protein More...
 
class  ProteomicsData
 Storage of proteomics data. More...
 
class  ProteomicsEMAlignmentAtomic
 Align proteomics graph to EM density map. More...
 
class  RadiusOfGyrationRestraint
 Ensure the radius of gyration of particles fits the predicted one. More...
 
class  RigidLeavesRefiner
 Return all rigid body members that are also hierarchy leaves. More...
 
class  SettingsData
 Holds header data for optimization. More...
 
class  WeightedExcludedVolumeRestraint
 Calculate score based on fit to EM map. More...
 

Typedefs

typedef IMP::Vector
< AlignmentParams > 
AlignmentParamsList
 
typedef IMP::Vector< AnchorsDataAnchorsDataList
 
typedef std::map< IntPair, int > CEdges
 
typedef IMP::Vector
< ComplementarityParams > 
ComplementarityParamsList
 
typedef IMP::Vector
< IMP::Pointer
< ComponentHeader > > 
ComponentHeaders
 
typedef IMP::Vector
< IMP::WeakPointer
< ComponentHeader > > 
ComponentHeadersTemp
 
typedef IMP::Vector
< ConnectivityParams > 
ConnectivityParamsList
 
typedef
IMP::algebra::DenseGrid3D
< double > 
DensGrid
 
typedef IMP::Vector
< IMP::Pointer
< DensityDataPoints > > 
DensityDataPointsList
 
typedef IMP::Vector
< IMP::WeakPointer
< DensityDataPoints > > 
DensityDataPointsListTemp
 
typedef IMP::Vector< DominoParams > DominoParamsList
 
typedef IMP::Vector
< IMP::Pointer< Ensemble > > 
Ensembles
 
typedef IMP::Vector
< IMP::WeakPointer< Ensemble > > 
EnsemblesTemp
 
typedef IMP::Vector< EVParams > EVParamsList
 
typedef IMP::Vector
< FiltersParams > 
FiltersParamsList
 
typedef IMP::Vector
< FittingParams > 
FittingParamsList
 
typedef IMP::Vector
< FittingSolutionRecord
FittingSolutionRecords
 
typedef IMP::Vector
< FragmentsParams > 
FragmentsParamsList
 
typedef IMP::Vector
< IMP::Pointer
< ProbabilisticAnchorGraph > > 
ProbabilisticAnchorGraphs
 
typedef IMP::Vector
< IMP::WeakPointer
< ProbabilisticAnchorGraph > > 
ProbabilisticAnchorGraphsTemp
 
typedef IMP::Vector
< ProteinRecordData > 
ProteinRecordDataList
 
typedef IMP::Vector
< ProteinsAnchorsSamplingSpace
ProteinsAnchorsSamplingSpaces
 
typedef IMP::Vector
< IMP::Pointer
< ProteomicsEMAlignmentAtomic > > 
ProteomicsEMAlignmentAtomics
 
typedef IMP::Vector
< IMP::WeakPointer
< ProteomicsEMAlignmentAtomic > > 
ProteomicsEMAlignmentAtomicsTemp
 
typedef IMP::Vector< RogParams > RogParamsList
 
typedef IMP::Vector< XlinkParams > XlinkParamsList
 

Functions

void add_surface_index (core::Hierarchy mhd, Float apix, FloatKey shell_key=FloatKey("surf_ind"), FloatKey radius_key=core::XYZR::get_radius_key(), FloatKey weight_key=atom::Mass::get_mass_key())
 Add shell index to leaves. More...
 
FittingSolutionRecords convert_em_to_multifit_format (const em::FittingSolutions &em_fits)
 
algebra::Transformation3Ds convert_multifit_format_to_transformations (const FittingSolutionRecords &recs)
 
em::FittingSolutions convert_multifit_to_em_format (const FittingSolutionRecords &multifit_fits)
 
FittingSolutionRecords convert_transformations_to_multifit_format (const algebra::Transformation3Ds &trans)
 
atom::Hierarchy create_coarse_molecule_from_density (em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius)
 Coarsen a density map based on voxels clustering. More...
 
em::DensityMapcreate_hit_map (core::RigidBody rb, Refiner *rb_ref, const FittingSolutionRecords &sols, em::DensityMap *damp)
 
IMP::Restraintcreate_weighted_excluded_volume_restraint (core::RigidBody rb1, core::RigidBody rb2, FloatKey shell_key=FloatKey("surf_ind"))
 Create a weighted excluded volume restraint between two rigid bodies. More...
 
multifit::FittingSolutionRecords fft_based_rigid_fitting (atom::Hierarchy mol2fit, em::DensityMap *dmap, double density_threshold, double angle_sampling_interval_rad)
 FFT fit of a molecule in the density. More...
 
float get_actual_radius_of_gyration (ParticlesTemp ps)
 
IntsList get_anchor_indices_matching_secondary_structure (const AnchorsData &ad, const atom::SecondaryStructureResidues &ssrs, Float max_rmsd=0.7)
 Get lists of anchors that match a sequence of secondary structures. More...
 
void get_anchors_for_density (em::DensityMap *dmap, int number_of_means, float density_threshold, std::string pdb_filename, std::string cmm_filename, std::string seg_filename, std::string txt_filename)
 Generate anchors in several formats for a given density map. More...
 
float get_approximated_radius (int len)
 
float get_approximated_radius_of_gyration (int len)
 
FittingSolutionRecords get_close_to_point (const FittingSolutionRecords &fit_sols, atom::Hierarchy mh, IMP::Particle *ap, Float dist)
 prune solutions by distance to an anchor point More...
 
IntsList get_connected_components (em::DensityMap *dmap, float threshold, float edge_threshold)
 Return connected components based on density values. More...
 
ProteinsAnchorsSamplingSpace get_part_of_sampling_space (const ProteinsAnchorsSamplingSpace &prots_ss, const Strings &prot_names)
 Get the sampling space of few of the proteins. More...
 
multifit::SettingsDataget_partial_assembly_setting_data (multifit::SettingsData *prots_sd, const Strings &prot_names)
 Get the assembly data for a few of the proteins. More...
 
ProteomicsDataget_partial_proteomics_data (const ProteomicsData *pd, const Strings &prot_names)
 
algebra::Vector3Ds get_points_close_to_molecule (const atom::Hierarchy &mh, const algebra::Vector3Ds points, Float max_dist)
 
algebra::Vector3Ds get_points_far_from_molecule (const atom::Hierarchy &mh, const algebra::Vector3Ds points, Float max_dist)
 
algebra::Vector3D get_segment_maximum (const DataPointsAssignment &dpa, em::DensityMap *dmap, int segment_id)
 
algebra::Vector3D get_segment_maximum (const DataPointsAssignment &dpa, DensGrid *dmap, int segment_id)
 
void get_segmentation (em::DensityMap *dmap, double apix, double density_threshold, int num_means, const std::string pdb_filename, const std::string cmm_filename, const std::string seg_filename, const std::string txt_filename)
 Segment a density map using the anchor graph. More...
 
em::DensityMapgrid2map (const DensGrid &dg, float spacing)
 
Ensembleload_ensemble (multifit::SettingsData *sd, Model *mdl, const ProteinsAnchorsSamplingSpace &mapping_data)
 
AnchorsData molecule2anchors (atom::Hierarchy mh, int k)
 
em::FittingSolutions pca_based_rigid_fitting (core::RigidBody rb, Refiner *rb_refiner, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis())
 Compute fitting scores for a given set of rigid transformations. More...
 
em::FittingSolutions pca_based_rigid_fitting (ParticlesTemp ps, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis())
 Compute fitting scores for a given set of rigid transformations. More...
 
AnchorsData read_anchors_data (const char *txt_filename)
 
std::pair< algebra::Vector3Ds,
CEdges > 
read_cmm (const std::string &cmm_filename)
 
FittingSolutionRecords read_fitting_solutions (const char *fitting_fn)
 Fitting solutions reader. More...
 
IntsList read_paths (const char *txt_filename, int max_paths=INT_MAX)
 Read paths. More...
 
ProteinsAnchorsSamplingSpace read_protein_anchors_mapping (multifit::ProteomicsData *prots, const std::string &anchors_prot_map_fn, int max_paths=INT_MAX)
 
ProteomicsDataread_proteomics_data (const char *proteomics_fn)
 Proteomics reader. More...
 
SettingsDataread_settings (const char *filename)
 
em::DensityMapremove_background (em::DensityMap *dmap, float threshold, float edge_threshold)
 Returns a map containing all density without the background. More...
 
void write_chimera (const std::string &chimera_filename, const DataPointsAssignment &dpa)
 
void write_cmm (const std::string &cmm_filename, const std::string &marker_set_name, const AnchorsData &dpa)
 
void write_connolly_surface (atom::Atoms atoms, TextOutput fn, float density, float probe_radius)
 Write the Connolly surface for a set of atoms to a file. More...
 
void write_fitting_solutions (const char *fitting_fn, const FittingSolutionRecords &fit_sols, int num_sols=-1)
 Write fitting solutions to a file. More...
 
void write_markers (const algebra::PrincipalComponentAnalysisD< 3 > &pca, std::ostream &out)
 
void write_paths (const IntsList &paths, const std::string &txt_filename)
 
void write_pdb (const std::string &pdb_filename, const DataPointsAssignment &dpa)
 
void write_protein_anchors_mapping (const std::string &anchors_prot_map_fn, const std::string &anchors_fn, const std::vector< std::pair< String, String > > &prot_paths)
 
void write_protein_anchors_mapping (const std::string &anchors_prot_map_fn, const ProteinsAnchorsSamplingSpace &pa, const Strings &prot_names)
 
void write_segment_as_mrc (em::DensityMap *dmap, const DataPointsAssignment &dpa, int segment_id, Float resolution, Float apix, const std::string &filename)
 
void write_segment_as_pdb (const DataPointsAssignment &dpa, int segment_id, const std::string &filename)
 
void write_segments_as_mrc (em::DensityMap *dmap, const DataPointsAssignment &dpa, Float resolution, Float apix, Float threshold, const std::string &filename)
 Write segments in MRC format. More...
 
void write_segments_as_pdb (const DataPointsAssignment &dpa, const std::string &filename)
 
void write_settings (const char *filename, const SettingsData *sd)
 
void write_txt (const std::string &txt_filename, const AnchorsData &ad)
 

Standard module functions

All IMP modules have a set of standard functions to help get information about the module and about files associated with the module.

std::string get_module_version ()
 
std::string get_module_name ()
 
std::string get_data_path (std::string file_name)
 Return the full path to one of this module's data files. More...
 
std::string get_example_path (std::string file_name)
 Return the full path to one of this module's example files. More...
 

Typedef Documentation

typedef IMP::Vector< AlignmentParams > IMP::multifit::AlignmentParamsList

Pass or store a set of AlignmentParams .

Definition at line 322 of file AlignmentParams.h.

Pass or store a set of AnchorsData .

Definition at line 89 of file anchors_reader.h.

typedef IMP::Vector< ComplementarityParams > IMP::multifit::ComplementarityParamsList

Pass or store a set of ComplementarityParams .

Definition at line 269 of file AlignmentParams.h.

A vector of reference-counting object pointers.

Definition at line 73 of file SettingsData.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
ComponentHeader

Definition at line 73 of file SettingsData.h.

typedef IMP::Vector< ConnectivityParams > IMP::multifit::ConnectivityParamsList

Pass or store a set of ConnectivityParams .

Definition at line 95 of file AlignmentParams.h.

A vector of reference-counting object pointers.

Definition at line 60 of file DensityDataPoints.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
DensityDataPoints

Definition at line 60 of file DensityDataPoints.h.

Pass or store a set of DominoParams .

Definition at line 48 of file AlignmentParams.h.

A vector of reference-counting object pointers.

Definition at line 49 of file ensemble_analysis.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
Ensemble

Definition at line 49 of file ensemble_analysis.h.

Pass or store a set of EVParams .

Definition at line 186 of file AlignmentParams.h.

Pass or store a set of FiltersParams .

Definition at line 209 of file AlignmentParams.h.

Pass or store a set of FittingParams .

Definition at line 235 of file AlignmentParams.h.

typedef IMP::Vector< FragmentsParams > IMP::multifit::FragmentsParamsList

Pass or store a set of FragmentsParams .

Definition at line 123 of file AlignmentParams.h.

A vector of reference-counting object pointers.

Definition at line 67 of file anchor_graph.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
ProbabilisticAnchorGraph

Definition at line 67 of file anchor_graph.h.

typedef IMP::Vector< ProteinRecordData > IMP::multifit::ProteinRecordDataList

Pass or store a set of ProteinRecordData .

Definition at line 68 of file proteomics_reader.h.

A vector of reference-counting object pointers.

Definition at line 115 of file proteomics_em_alignment_atomic.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
ProteomicsEMAlignmentAtomic

Definition at line 115 of file proteomics_em_alignment_atomic.h.

Pass or store a set of RogParams .

Definition at line 143 of file AlignmentParams.h.

Pass or store a set of XlinkParams .

Definition at line 72 of file AlignmentParams.h.

Function Documentation

void IMP::multifit::add_surface_index ( core::Hierarchy  mhd,
Float  apix,
FloatKey  shell_key = FloatKey("surf_ind"),
FloatKey  radius_key = core::XYZR::get_radius_key(),
FloatKey  weight_key = atom::Mass::get_mass_key() 
)

Add shell index to leaves.

Parameters
[in]mhdthe Hierarchy to modify
[in]apixthe resolution of the surface
[in]shell_keythe Key used to store the shell index
[in]radius_keythe Key used for particle radius
[in]weight_keythe Key used for particle weight (e.g. mass)
Note
we assume that the leaves are xyz particles
atom::Hierarchy IMP::multifit::create_coarse_molecule_from_density ( em::DensityMap *  dmap,
float  dens_threshold,
int  num_beads,
Model *  mdl,
float  bead_radius 
)

Coarsen a density map based on voxels clustering.

Parameters
[in]dmapthe density map to coarsen
[in]dens_thresholduse only voxels above this threshold for clustering
[in]num_beadsthe number of beads
[in]mdlmodel to add the new molecule to
[in]bead_radiusbead radius
IMP::Restraint* IMP::multifit::create_weighted_excluded_volume_restraint ( core::RigidBody  rb1,
core::RigidBody  rb2,
FloatKey  shell_key = FloatKey("surf_ind") 
)

Create a weighted excluded volume restraint between two rigid bodies.

Parameters
[in]rb1the first rigid body
[in]rb2the second rigid body
[in]shell_keythe attribute that stored the particles surface level with respect to its molecule
multifit::FittingSolutionRecords IMP::multifit::fft_based_rigid_fitting ( atom::Hierarchy  mol2fit,
em::DensityMap *  dmap,
double  density_threshold,
double  angle_sampling_interval_rad 
)

FFT fit of a molecule in the density.

Parameters
[in]mol2fita rigid body molecule to fit
[in]dmapthe map to fit into
[in]density_thresholdignore density below this value
[in]angle_sampling_interval_radsampling internal in radians
IntsList IMP::multifit::get_anchor_indices_matching_secondary_structure ( const AnchorsData &  ad,
const atom::SecondaryStructureResidues &  ssrs,
Float  max_rmsd = 0.7 
)

Get lists of anchors that match a sequence of secondary structures.

Parameters
[in]adThe AnchorsData
[in]ssrsThe SecondaryStructureResidue particles to match
[in]max_rmsdSecondaryStructureResidue match must be below this value (0.816 is rmsd of known SSE to random)
void IMP::multifit::get_anchors_for_density ( em::DensityMap *  dmap,
int  number_of_means,
float  density_threshold,
std::string  pdb_filename,
std::string  cmm_filename,
std::string  seg_filename,
std::string  txt_filename 
)

Generate anchors in several formats for a given density map.

FittingSolutionRecords IMP::multifit::get_close_to_point ( const FittingSolutionRecords &  fit_sols,
atom::Hierarchy  mh,
IMP::Particle ap,
Float  dist 
)

prune solutions by distance to an anchor point

Parameters
[in]fit_solsinitial fitting solutions
[in]mhthe molecule the fitting solutions apply for
[in]apanchor point for which the transformed mh (fit) should be close to
[in]distall fits such that the distance between ap and the fit center is smaller than dist will be included
Returns
the pruned fitting solutions
IntsList IMP::multifit::get_connected_components ( em::DensityMap *  dmap,
float  threshold,
float  edge_threshold 
)

Return connected components based on density values.

Parameters
[in]dmapthe density map to analyze
[in]thresholdconsider only voxels above this threshold
[in]edge_thresholdan edge is added between two neighboring voxels if their density difference is below this threshold
Returns
List of indexes for each connected component
std::string IMP::multifit::get_data_path ( std::string  file_name)

Return the full path to one of this module's data files.

To read the data file "data_library" that was placed in the data directory of this module, do something like

std::ifstream in(IMP::multifit::get_data_path("data_library"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note
Each module has its own data directory, so be sure to use this function from the correct module.
std::string IMP::multifit::get_example_path ( std::string  file_name)

Return the full path to one of this module's example files.

To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like

std::ifstream in(IMP::multifit::get_example_path("example_protein.pdb"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note
Each module has its own example directory, so be sure to use this function from the correct module.
ProteinsAnchorsSamplingSpace IMP::multifit::get_part_of_sampling_space ( const ProteinsAnchorsSamplingSpace &  prots_ss,
const Strings &  prot_names 
)

Get the sampling space of few of the proteins.

multifit::SettingsData* IMP::multifit::get_partial_assembly_setting_data ( multifit::SettingsData *  prots_sd,
const Strings &  prot_names 
)

Get the assembly data for a few of the proteins.

algebra::Vector3Ds IMP::multifit::get_points_close_to_molecule ( const atom::Hierarchy &  mh,
const algebra::Vector3Ds  points,
Float  max_dist 
)

Given a molecule and a set of points, return the indexes of the points that are close to the molecule (up to max_dist) and the res

void IMP::multifit::get_segmentation ( em::DensityMap *  dmap,
double  apix,
double  density_threshold,
int  num_means,
const std::string  pdb_filename,
const std::string  cmm_filename,
const std::string  seg_filename,
const std::string  txt_filename 
)

Segment a density map using the anchor graph.

All voxels above the threshold are segmented into the given number of clusters, and neighboring clusters are linked.

Parameters
[in]dmapthe density map to segment
[in]apixthe map spacing in angstroms per pixel
[in]density_thresholdconsider only voxels over this threshold
[in]num_meansthe number of segments to generate
[in]pdb_filenamewrite cluster centers as CA atoms in PDB format
[in]cmm_filenameif not empty, write clusters in CMM format
[in]seg_filenameif not empty, write segments in MRC format
[in]txt_filenameif not empty, write anchors in text format
em::FittingSolutions IMP::multifit::pca_based_rigid_fitting ( core::RigidBody  rb,
Refiner *  rb_refiner,
em::DensityMap *  em_map,
Float  threshold,
FloatKey  wei_key = atom::Mass::get_mass_key(),
algebra::PrincipalComponentAnalysis  dens_pca_input = algebra::PrincipalComponentAnalysis() 
)

Compute fitting scores for a given set of rigid transformations.

Fit a protein to its density by principal component matching

Parameters
[in]rbThe rigid body to be fitted
[in]rb_refinerThe rigid body refiner
[in]em_mapThe density map to fit to
[in]thresholdUse voxels above this threshold for PCA calculations
[in]wei_keyThe weight key of the particles in the rigid body
[in]dens_pca_inputprovide precalculated em_map PCA is available
Returns
fitting solutions
Note
the function assumes the density map holds its density
em::FittingSolutions IMP::multifit::pca_based_rigid_fitting ( ParticlesTemp  ps,
em::DensityMap *  em_map,
Float  threshold,
FloatKey  wei_key = atom::Mass::get_mass_key(),
algebra::PrincipalComponentAnalysis  dens_pca_input = algebra::PrincipalComponentAnalysis() 
)

Compute fitting scores for a given set of rigid transformations.

Fit a protein to its density by principal component matching

Parameters
[in]psThe particles to fit (treated as rigid)
[in]em_mapThe density map to fit to
[in]thresholdUse voxels above this threshold for PCA calculations
[in]wei_keyThe weight key of the particles in the rigid body
[in]dens_pca_inputprecalculated em_map PCA
Returns
fitting solutions
Note
the function assumes the density map holds its density
FittingSolutionRecords IMP::multifit::read_fitting_solutions ( const char *  fitting_fn)

Fitting solutions reader.

IntsList IMP::multifit::read_paths ( const char *  txt_filename,
int  max_paths = INT_MAX 
)

Read paths.

Note
Notice that for the function to read the last line it should end with
ProteomicsData* IMP::multifit::read_proteomics_data ( const char *  proteomics_fn)

Proteomics reader.

em::DensityMap* IMP::multifit::remove_background ( em::DensityMap *  dmap,
float  threshold,
float  edge_threshold 
)

Returns a map containing all density without the background.

Parameters
[in]dmapthe density map to segment
[in]thresholdconsider only voxels above this threshold
[in]edge_thresholdconsider only voxels above this threshold
Returns
the segmented map
void IMP::multifit::write_connolly_surface ( atom::Atoms  atoms,
TextOutput  fn,
float  density,
float  probe_radius 
)

Write the Connolly surface for a set of atoms to a file.

void IMP::multifit::write_fitting_solutions ( const char *  fitting_fn,
const FittingSolutionRecords &  fit_sols,
int  num_sols = -1 
)

Write fitting solutions to a file.

Parameters
[in]fitting_fnthe fitting filename
[in]fit_solsthe fitting solutions to write to file
[in]num_solsoptional, only write the first num_sols fits.
void IMP::multifit::write_segments_as_mrc ( em::DensityMap *  dmap,
const DataPointsAssignment &  dpa,
Float  resolution,
Float  apix,
Float  threshold,
const std::string &  filename 
)

Write segments in MRC format.

Note
segments are written as filename_0.mrc
an additional file filename.cmd is generated for easy loading of all segments