IMP modules provide a number of command line tools. These are listed below under their parent module:

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::atom
- pdb_check: Check a PDB file for problems.
- ligand_score: Score ligand poses.
- ligand_score_multiple: Score ligand poses from docking output.
IMP::cnmultifit
- cnmultifit: command line tool
IMP::em
- 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::em2d
- create_single_particle_images: Create single particle images, either noiseless, noisy, or purenoise. Run without argument for full options list.
IMP::example
- imp_example_app: This is an example application (command line tool).
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::kinematics
- rrt_sample: Sample protein conformations using rapidly exploring random tree (RRT).
- rrt_ccd: Sample protein loop conformations using rapidly exploring random tree (RRT).
- rmsd_cluster: RMSD based clustering of conformations
IMP::multi_state
- multi_foxs: Command line tool to enumerate multi-state models with SAXS profiles.
- multi_foxs_combination: Command line tool to enumerate additions (such as glycans or ions) to a model with SAXS profiles.
IMP::multifit
- multifit: command line tool
- complex_to_anchor_graph: Build an anchor graph from a PDB file.
IMP::npctransport
- fg_simulation: run NPC transport simulations
IMP::rmf
- 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::sampcon
- imp_sampcon: sampling exhaustiveness test
IMP::saxs
- cluster_profiles: Cluster SAXS profiles.
- compute_chi: Calculate chi value for SAXS profiles.
- compute_vr: Calculate volatility ratio for SAXS profiles.
- compute_rg: Compute radius of gyration from SAXS profiles.
- validate_profile: Validate SAXS profiles.
- weight_profiles: Weighting of the profiles.
IMP::saxs_merge
- saxs_merge: A method for merging SAXS profiles using Gaussian processes.
IMP::spb
- spb: This is the main executable for running sampling using Well-Tempered Ensemble Replica Exchange, based on FRET, yeast two-hybrid and other restraints.
- spb_analysis: After running sampling, we need to rescore the final ensemble (all models at 1 K) based on the EM2D score.
- spb_cluster: Models are clustered taking their weight into account. Distance threshold-based clustering is performed with a 1.5 nm threshold.
- spb_density_perbead: To better localize the protein termini, localization density is calculated per bead per protein for a given cluster.
- spb_test_score: Code to output the restraint values of a model. Takes 2 RMFs as input: one containing structural coordinations and another containing ISD values.