All IMP command line tools

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.
• IMP::multifit
  • multifit: command line tool
  • complex_to_anchor_graph: Build an anchor graph from a PDB file.
• 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::saxs
  • cluster_profiles: Cluster SAXS profiles.
  • compute_chi: Calculate chi value for SAXS profiles.
  • compute_vr: Calculate volatility ratio for SAXS profiles.
  • 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.

See also the command line tools provided by RMF.