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These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the SEA complex using 188 DSS chemical cross-links and 23 composites from affinity purification.

First, MODELLER is used to generate initial structures for the individual components where reliable templates are available. Then, IMP / PMI are used to model these components using the DSS crosslinks and the affinity purification data for the entire SEA complex.

The scripts work with the 65734ec version (develop branch) of IMP and the 47dafcc version (develop branch) of PMI.

A full description of the scripts can be found in Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.

List of files and directories:

  • pdb contains all input crystal structures that were deposited in PDB.

  • scripts

    • The main modeling script with 1:3 stoichiometry and rotational symmetry

    • MODELLER/Npr2 MODELLER scripts and output comparative models of Npr2

    • MODELLER/Npr3 MODELLER scripts and output comparative models of Npr3

    • MODELLER/SEA1 MODELLER scripts and output comparative models of SEA1

    • MODELLER/SEA2 MODELLER scripts and output comparative models of SEA2

    • MODELLER/SEA3 MODELLER scripts and output comparative models of SEA3

    • MODELLER/SEA4 MODELLER scripts and output comparative models of SEA4

  • output/three_sym_cluster

    • Largest output cluster as a set of RMF files. Each file is named XX_REFINED_models_YY.rmf where XX identifies the run from which the model was taken and YY the frame number. For the publication, 885 runs were carried out.

    • global Localization densities in MRC format and a Chimera session file ( to display them.

Running the MODELLER scripts:

  • cd scripts/MODELLER/Npr2 && python : Npr2 9-127
  • cd scripts/MODELLER/Npr2 && python : Npr2 257-327
  • cd scripts/MODELLER/Npr2 && python : Npr2 563-610
  • cd scripts/MODELLER/Npr3 && python : Npr3 322-438
  • cd scripts/MODELLER/Npr3 && python : Npr3 531-577
  • cd scripts/MODELLER/Npr3 && python : Npr3 1-31
  • cd scripts/MODELLER/Npr3 && python : Npr3 950-988
  • cd scripts/MODELLER/Npr3 && python : Npr3 1083-1140
  • cd scripts/MODELLER/SEA1 && python : SEA1 101-275
  • cd scripts/MODELLER/SEA1 && python : SEA1 279-473
  • cd scripts/MODELLER/SEA1 && python : SEA1 1178-1273
  • cd scripts/MODELLER/SEA2 && python : SEA2 127-520
  • cd scripts/MODELLER/SEA2 && python : SEA2 1280-1341
  • cd scripts/MODELLER/SEA3 && python : SEA3 54-424
  • cd scripts/MODELLER/SEA3 && python : SEA3 430-536
  • cd scripts/MODELLER/SEA3 && python : SEA3 1092-1139
  • cd scripts/MODELLER/SEA4 && python : SEA4 45-426
  • cd scripts/MODELLER/SEA4 && python : SEA4 659-835
  • cd scripts/MODELLER/SEA4 && python : SEA4 942-1032

Running the IMP/PMI scripts for the SEA complex:

To produce a single model with 1:3 stoichiometry and rotational symmetry, as in the publication, use the script:

mkdir modeling
cd modeling
../ 50000 20000 3 True

This script in turn runs scripts/, which if desired can be run with different options to explore other representations and sampling options.

For the publication, this script was run 885 times to generate the final ensemble, which was then clustered to produce the 340 models in the output directory.


Author(s): Seung Joong Kim, Riccardo Pellarin, and Peter Cimermancic

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: No