- Brownian dynamics tutorial
- Introduction to Brownian Dynamics (BD) and setting up and running BD simulations in IMP.
- Fitting against SAXS data with FoXS and MultiFoXS
- This covers using the FoXS and MultiFoXS tools in IMP to fit one or more structures against small angle X-ray (SAXS) data.
- Cross-linking tutorial
- This introduces the functionality in IMP to handle cross-linking data and apply it in modeling.
- Integrative spatiotemporal modeling in IMP
- This tutorial introduces the IMP.spatiotemporal module, which can be used to compute step-wise models of biomolecular dynamics, which are in agreement with experimental data by construction.
- Modeling of an actin complex with PMI
- This demonstratates integrative modeling using the PMI interface by modeling the complex of actin and tropomodulin-gelsolin chimera using SAXS, EM, crosslinking, crystal structures of the individual domains and physical principles.
- PMI RNAPII Modeling Tutorial
- This tutorial introduces the Python Modeling Interface (PMI), a set of tools designed to handle all steps of the modeling protocol, and demonstrates it by modeling the stalk of RNA Polymerase II using cross-linking, electron microscopy, and x-ray crystallography data.
- Introduction to writing IMP code
- This covers creating a new IMP module, and writing a new restraint in C++.
- Profiling IMP applications
- This introduces CPU profiling of IMP code with Google's gperftools package, to track down where time is being spent.
- Using IMP as a C++ library
- This covers using IMP as a C++ library in other C++ projects.
- Debugging IMP with Valgrind
- This shows how to use Valgrind to find memory leaks and other programming errors in IMP C++ code.
- Deposition of IMP models
- This covers the procedure for depositing integrative modeling studies in the PDB-IHM database in mmCIF format.
Writing new tutorials
To write a new tutorial, follow
these instructions.
