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GroEL

Modeling of the bacterial molecular chaperone GroEL using 3D EM data and cnmultifit PubMed logo

tickVerified to work with the latest stable IMP release (2.11.1). The files are also available at GitHub.
Additional software needed to use these files: IMP MODELLER numpy 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 numpy

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

module load imp modeller python/numpy
Tags EM density map MODELLER MultiFit

DOI

These scripts demonstrate the use of IMP, MODELLER and Chimera in the modeling of the bacterial molecular chaperone GroEL. First, MODELLER is used to generate structures for the individual components in the GroEL complex. Then, IMP is used to fit these components together into the electron microscopy density map of the entire complex.

A full description of the scripts can be found in Macromolecular assembly structures by comparative modeling and electron microscopy.

Steps

First, make a directory for the output by running mkdir output. Output files that were generated when these scripts were run for the first time are also provided, in the precalculate_results directory. Then, the scripts can be run in order:

  1. Template identification: scripts/script1_build_profile.py
  2. Template(s) selection by sequence: scripts/script2_compare_templates.py
  3. Density map segmentation: scripts/script3_density_segmentation.py
  4. Template selection by fitting to a density map: scripts/script4_score_templates_by_cc.py
  5. Template alignment: scripts/script5_template_alignment.py
  6. Model building and assessment: scripts/script6_model_building_and_assessment.py and scripts/script7_pairwise_rmsd.py
  7. Multiple fitting into a density map: scripts/script8_split_density.py and scripts/script9_symmetric_multiple_fitting.py

Info

Author(s): Keren Lasker

Version: 1.0

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: No

Publications: