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TFIIH complex

Modeling of the TFIIH complex using chemical cross-links and electron microscopy (EM) density maps PubMed logo

tickVerified to work with the latest stable IMP release (2.9.0). The files are also available at GitHub.
Additional software needed to use these files: IMP scikit-learn matplotlib install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp scikit-learn matplotlib

UCSF logo To set up the environment on the UCSF QB3 cluster to run this system, run:

module load imp python/scikit python/matplotlib
Tags chemical crosslinks EM density map PMI

DOI

These scripts demonstrate the use of IMP and PMI in the modeling of the TFIIH complex using chemical cross-links and electron microscopy (EM) density maps.

For the publication, the following versions of IMP and PMI were used:

The files should also work with a recent version of IMP (see below).

List of files and directories:

Running the IMP/PMI scripts for the TFIIH

Note that in both yeast and human cases, the script analyze.py has many different uses: calculating the top 10% of scores, getting density maps, calculating the percentage of violated constraints, getting PDB files for the models, clustering the top scoring models, getting contact maps etc.

To use each of these functions, one can just comment out the remaining part of the code and retain only the neccessary function each time.

Note that clustering is a 2 step process for the human modeling: the cluster subroutine in analyze.py outputs the distance matrix and the clustering.py script run on that distance matrix produces the actual clusters.

Information

Author(s): Peter Cimermančič, Shruthi Viswanath, Riccardo Pellarin, Charles Greenberg

Date: September 3rd, 2015

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Last known good IMP version: build info build info

Testable: Yes.

Publications: