imp_analysis_tutorial

This tutorial demonstrates the analysis of integrative modeling results using the Integrative Modeling Platform (IMP).

./rnapolii - Improved analysis routine for the PMI modeling tutorial of the RNA Polymerase III stalk.

Citations: In review

Installation and Dependencies

Getting the tutorial code and data

This tutorial can be downloaded from this page or the command line using git clone github.com/salilab/imp_analysis_tutorial

Submodules must be downloaded by navigating to the tutorial main directory and running

git submodule init
git submodule update

Installing IMP and dependencies

The tutorial requires IMP v2.13 (April 2020) or later to run correctly.

---Using anaconda---

The simplest way to install and run IMP and this tutorial is using anaconda.

Once installed, IMP and required dependencies can be installed using the following commands

conda install -c salilab imp pyrmsd
conda install numpy scikit-learn matplotlib pandas
conda install -c conda-forge hdbscan

---Using stand-alone IMP---

IMP binaries or source code are available for download.

Python 3.X is recommended to run IMP. Dependencies can be installed via pip:

pip install numpy scikit-learn matplotlib pandas hdbscan

A modified version of pyRMSD must be installed as well:

• pyRMSD

Running the tutorial

Navigate to ./rnapolii and continue from the rnapolii README