IMP Manual

This manual covers the installation of the Integrative Modeling Platform (IMP) software and its basic usage. It is targeted mainly at users, i.e. people that want to use existing IMP functionality. Later sections of this manual introduce more technical details to those that want to modify the IMP source code to develop new methods (developers). The Reference Guide may also be useful for such developers.

Users that want to get started quickly with modeling a real biological complex might want to skip ahead to Modeling of complexes using IMP::pmi.

Note

This documentation is for version 2.9.0 of IMP. For documentation for other versions, please see the documentation page at the IMP website.

• Installation
• Introduction to integrative modeling
• Design of IMP
• Chimera tools and web services
• Using command line tools
  • FoXS: fitting structures against SAXS data
  • MultiFoXS: determination of multi-state models
  • Integrative docking: combining experimental data with computational pairwise docking
  • Conformational sampling: sampling antibody conformations using the rapidly exploring random tree (RRT) algorithm
  • EMageFit: solution of a complex structure using subunit structures and EM class averages
  • MultiFit: solution of a complex structure using subunit structures and a cryo-EM density map
  • CNMultiFit: solution of symmetric complexes using a cryo-EM density map
  • SAXSMerge: merging multiple SAXS profiles
• Modeling of complexes using IMP::pmi
  • Stage 1: Gathering of data
  • Stage 2: Representation of the system
  • Stage 3: Sampling
  • Stage 4a: Analysis part 1
  • Stage 4b: Analysis part 2
• The IMP C++/Python library
  • Overview
  • Example of using the library
  • Glossary
  • Logging
  • Runtime checks
  • Units
  • Naming and interface conventions
  • Parallelization
• Frequently asked questions (FAQ)
• Contributing to IMP
• Bug reports
• Applying IMP to a new biological system
• Developing the IMP source code
  • Developer setup
  • Directory structure
  • Coding conventions
  • Good programming practices
  • IMP gotchas
  • Writing new code
  • Working with source control
  • Adding external dependencies
  • Design example
  • Tools for developers
  • Documenting your code
  • Debugging and testing your code
  • Writing examples
  • Exporting C++ code to Python
  • Code coverage
  • Profiling your code
  • Deprecation
  • Cross platform compatibility
  • Contributing code back to IMP
  • Supporting your code
  • Automated builds and checks
• Internals
  • Dependencies
  • Evaluation
  • Close pairs lists
  • RMF
  • Building
  • git submodules and subtrees
• Copyright and licenses
• Change history
• Publications