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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 is used to model these components using the DSS/EDC crosslinks and the affinity purification data for the entire SEA complex.

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 3 crystal interfaces

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

  • 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 SEA complex script:

with 1:3 stoichiometry and 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: