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Nup84 Complex

Modeling of the Nup84 subcomplex of the Nuclear Pore Complex PubMed logo PDB-Dev

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 MODELLER scikit-learn matplotlib biopython 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 modeller scikit-learn matplotlib biopython

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

module load imp modeller python/scikit python/matplotlib
Tags chemical crosslinks EM class average MODELLER PMI

DOI

These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the Nup84 complex using 286 DSS/EDC chemical cross-links and an electron microscopy (EM) 2D class average.

First, MODELLER is used to generate initial structures for the individual components in the Nup84 complex. Then, IMP is used to model these components using DSS/EDC crosslinks and the electron microscopy 2D class average for the entire Nup84 complex.

The modeling protocol will work with a default build of IMP, but for most effective sampling, IMP should be built with MPI so that replica exchange can be used.

List of files and directories:

Running the MODELLER scripts:

Running the IMP/PMI scripts for the Nup84 complex:

with 3 crystal interfaces:

with no crystal interfaces:

Next, merge and cluster the resulting models (this script can also be used to combine results from multiple independent runs):

Finally, analyze the resulting clusters:

Information

Author(s): Riccardo Pellarin, Elina Tjioe, and Seung Joong Kim

Date: October 6th, 2014

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.

Parallelizeable: Yes

Publications:

*These authors contributed equally to this work as co-first authors.