integrativemodeling/sea

Modeling of the SEA complex

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

  • sj_SEA_multi_layers.py 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 (Chimera_three_sym.py) to display them.

Running the MODELLER scripts:

• cd scripts/MODELLER/Npr2 && python all_sjkim_final1.py : Npr2 9-127
• cd scripts/MODELLER/Npr2 && python all_sjkim_final2.py : Npr2 257-327
• cd scripts/MODELLER/Npr2 && python all_sjkim_final3.py : Npr2 563-610
• cd scripts/MODELLER/Npr3 && python all_sjkim_final1.py : Npr3 322-438
• cd scripts/MODELLER/Npr3 && python all_sjkim_final2.py : Npr3 531-577
• cd scripts/MODELLER/Npr3 && python all_sjkim_final3.py : Npr3 1-31
• cd scripts/MODELLER/Npr3 && python all_sjkim_final4.py : Npr3 950-988
• cd scripts/MODELLER/Npr3 && python all_sjkim_final5.py : Npr3 1083-1140
• cd scripts/MODELLER/SEA1 && python all_sjkim_final1.py : SEA1 101-275
• cd scripts/MODELLER/SEA1 && python all_sjkim_final2.py : SEA1 279-473
• cd scripts/MODELLER/SEA1 && python all_sjkim_final3.py : SEA1 1178-1273
• cd scripts/MODELLER/SEA2 && python all_sjkim_final1.py : SEA2 127-520
• cd scripts/MODELLER/SEA2 && python all_sjkim_final2.py : SEA2 1280-1341
• cd scripts/MODELLER/SEA3 && python all_sjkim_final1.py : SEA3 54-424
• cd scripts/MODELLER/SEA3 && python all_sjkim_final2.py : SEA3 430-536
• cd scripts/MODELLER/SEA3 && python all_sjkim_final3.py : SEA3 1092-1139
• cd scripts/MODELLER/SEA4 && python all_sjkim_final1.py : SEA4 45-426
• cd scripts/MODELLER/SEA4 && python all_sjkim_final2.py : SEA4 659-835
• cd scripts/MODELLER/SEA4 && python all_sjkim_final3.py : 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 run_qsub.sh script:

mkdir modeling
cd modeling
../run_qsub.sh 50000 20000 3 True

This script in turn runs scripts/sj_SEA_multi_layers.py, 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.

Information

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:

Testable: Yes.

Parallelizeable: No

Publications:

• Romain Algret, Javier Fernandez-Martinez, Yi Shi, Seung Joong Kim, Riccardo Pellarin, Peter Cimermancic, Emilie Cochet, Andrej Sali, Brian T. Chait, Michael P. Rout, and Svetlana Dokudovskaya, Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway, Molecular & Cellular Proteomics, 2014, mcp.M114.039388.

sea's Issues

Need script parameters and output files

@procyon777 , with some tweaks the IMP modeling script works with current IMP:

python sj_SEA_multi_layers.py -r 1000 -w 1.0 -x ../SEAcmplx_XL.txt -o models.rmf -s stat.out --REFINE False --copy 3 --sym False

What is still missing though is the set of parameters you used to do the actual modeling for the publication (it looks like you ran it once, maybe picked the best model, and used that as input for another round of modeling). Please update the README file with the necessary invocations of the script.

We also need the output files so we can visualize the localization densities and deposit representative models (top-scoring model? cluster centroid?) These don't necessarily need to go in the repository itself (e.g. if they're big). Just point me to where they are on disk and I'll archive them.