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Nuclear Pore Complex

Modeling of the yeast Nuclear Pore Complex PubMed logo PDB-Dev

crossWarning: these files have not yet been verified to work with the latest version of IMP. We will update this page when they have been. The files are also available at GitHub.
Additional software needed to use these files: IMP MODELLER 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

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

module load imp modeller
Tags affinity purification chemical crosslinks EM class average EM density map FoXS PMI X-ray

DOI

These scripts demonstrate the use of IMP in the modeling of the yeast NPC complex using diverse types of data as described in Seung Joong Kim, et al.'s 2018 NPC article published in Nature.

The scripts work with the IMP (version 2.6). A default build of IMP compiled with the IMP::npc module should work, but for most effective sampling, it should be built with MPI so that replica exchange can be used.

List of files and directories:

Compiling IMP with NPC-specific module:

Running the IMP scripts for the NPC complex:

  1. Inner-ring components (Nup157, Nup170, Nup188, Nup192, Nic96, Nup53, Nup59, Ndc1, Pom34, and Pom152 NTD)
  1. Outer-ring components (Nup82 and Nup84 complexes)

or job_test4.sh

Information

Author(s): Seung Joong Kim

License: CC-BY-SA-4.0. This work is freely available under the terms of the Creative Commons Attribution-ShareAlike 4.0 International License.

Last known good IMP version: build info build info

Publications: