Skip to content

Latest commit

 

History

History
93 lines (61 loc) · 4.66 KB

README.md

File metadata and controls

93 lines (61 loc) · 4.66 KB

SEA Complex

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

First, MODELLER is used to generate initial structures for the individual components where reliable templates are available. Then, IMP / PMI is used to model these components using the DSS/EDC 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 structures that were generated by MODELLER or deposited in PDB.

  • scripts

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

    • chimera_scripts/sea_density.cmd Chimera script to view all localization density files

    • MODELLER/Npr2 MODELLER scripts to generate comparative models of Npr2

    • MODELLER/Npr3 MODELLER scripts to generate comparative models of Npr3

    • MODELLER/SEA1 MODELLER scripts to generate comparative models of SEA1

    • MODELLER/SEA2 MODELLER scripts to generate comparative models of SEA2

    • MODELLER/SEA3 MODELLER scripts to generate comparative models of SEA3

    • MODELLER/SEA4 MODELLER scripts to generate comparative models of SEA4

  • outputs/pdbs the production will write the best scoring models into pdb files they are initialized and then updated as long as the calculation goes (They are the best 500 models, so at the beginning they are empty, since you haven't start the calculation yet)

  • outputs/rmfs the production will write the rmf3 files for lowest temperature replica.

  • stat.n.out log files. They contain all relevant numbers of the calculation.

Running the MODELLER scripts:

  • mod9.12 scripts/MODELLER/Npr2/all_sjkim_final1.py : Npr2 9-127
  • mod9.12 scripts/MODELLER/Npr2/all_sjkim_final2.py : Npr2 257-327
  • mod9.12 scripts/MODELLER/Npr2/all_sjkim_final3.py : Npr2 563-610
  • mod9.12 scripts/MODELLER/Npr3/all_sjkim_final1.py : Npr3 322-438
  • mod9.12 scripts/MODELLER/Npr3/all_sjkim_final2.py : Npr3 531-577
  • mod9.12 scripts/MODELLER/Npr3/all_sjkim_final3.py : Npr3 1-31
  • mod9.12 scripts/MODELLER/Npr3/all_sjkim_final4.py : Npr3 950-988
  • mod9.12 scripts/MODELLER/Npr3/all_sjkim_final5.py : Npr3 1083-1140
  • mod9.12 scripts/MODELLER/SEA1/all_sjkim_final1.py : SEA1 101-275
  • mod9.12 scripts/MODELLER/SEA1/all_sjkim_final2.py : SEA1 279-473
  • mod9.12 scripts/MODELLER/SEA1/all_sjkim_final3.py : SEA1 1178-1273
  • mod9.12 scripts/MODELLER/SEA2/all_sjkim_final1.py : SEA2 127-520
  • mod9.12 scripts/MODELLER/SEA2/all_sjkim_final2.py : SEA2 1280-1341
  • mod9.12 scripts/MODELLER/SEA3/all_sjkim_final1.py : SEA3 54-424
  • mod9.12 scripts/MODELLER/SEA3/all_sjkim_final2.py : SEA3 430-536
  • mod9.12 scripts/MODELLER/SEA3/all_sjkim_final3.py : SEA3 1092-1139
  • mod9.12 scripts/MODELLER/SEA4/all_sjkim_final1.py : SEA4 45-426
  • mod9.12 scripts/MODELLER/SEA4/all_sjkim_final2.py : SEA4 659-835
  • mod9.12 scripts/MODELLER/SEA4/all_sjkim_final3.py : SEA4 942-1032

Running the SEA complex script:

with 1:3 stoichiometry and rotational symmetry:

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: build info

Testable: Yes.

Parallelizeable: No

Publications: