IMP provides a number of applications (command line tools). These are listed below:

IMP.EMageFit
- emagefit: Run all steps of modeling
- emagefit_dock: Docking using the HEXDOCK program
- emagefit_cluster: Performs clustering of the solutions stored in a database file.
- emagefit_score: Scores a model using EM images.
- convert_spider_to_jpg: Image conversion utility for EMageFit.
IMP.cnmultifit_tools
- cnmultifit: Fit atomic structures into cyclic symmetric EM density maps.
IMP.em_tools
- estimate_threshold_from_molecular_mass: Estimate EM density threshold.
- map2pca: Write out density map principal components in cmm format.
- mol2pca: Write out protein principal components in cmm format.
- resample_density: Resample a density map.
- simulate_density_from_pdb: Samples a protein into a simulated 3D density map.
- view_density_header: Display the header information for a density map.
IMP.example_app
- imp_example_app: An example application.
IMP.foxs
- foxs: Determine small angle X-ray (SAXS) profiles.
IMP.integrative_docking
- idock: Pairwise docking incorporating additional data.
- saxs_score: Scoring with SAXS profile.
- em2d_score: Scoring with EM 2D class averages.
- em3d_score: Scoring with EM 3D density map.
- nmr_rtc_score: Scoring with NMR residue type content term (NMR-RTC).
- cross_links_score: Scoring with cross links detected by mass spectrometry.
- combine_scores: Combine scores for different data types.
- recompute_zscore: Recompute z-scores for combined scores.
- em3d_single_score: Score a single model with EM3D.
- em2d_single_score: Score a single model with EM2D.
- soap_score: Score models with SOAP.
- cross_links_single_score: Score a single model with cross links.
- interface_cross_links: Generate cross links for an interface.
- interface_rtc: Generate residue content for an interface.
IMP.ligand_score
- ligand_score: Score ligand poses.
IMP.multifit_tools
- multifit: Fit atomic structures into EM density maps.
- complex_to_anchor_graph: Build an anchor graph from a PDB file.
IMP.pdb_tools
- pdb_check: Check a PDB file for problems.
IMP.rmf_tools
- rmf_display: Export an RMF file to a viewer.
- pdb_rmf: Make an RMF file from a PDB.
- rmf_simplify: Create a simplified representation of a PDB.
IMP.saxs_merge
- saxs_merge: A method for merging SAXS profiles using Gaussian processes.
IMP.saxs_tools
- cluster_profiles: Cluster SAXS profiles.
- compute_chi: Calculate chi value for SAXS profiles.
- rg: Compute radius of gyration from SAXS profiles.
- validate_profile: Validate SAXS profiles.