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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:

  • data contains all relevant data, input structure, etc.

  • scripts

    • nup84.isd.modeling.withXrayInterface.py the main modeling script with 3 crystal interfaces

    • nup84.isd.modeling.py the main modeling script with no crystal interfaces

    • nup84.topology.withXrayInterface.py constructs Nup84 subunits with 3 crystal interfaces

    • nup84.topology.py constructs Nup84 subunits with no crystal interfaces

    • nup84.merge.py script to merge output files from all runs ; filter threshold on total score can be set here

    • vmd_scripts/rmdstt.tcl VMD script to launch RMSD Trajectory Tool window

    • vmd_scripts/nup84_3-xray_density.tcl VMD script to calculate localization density for Nup84 with 3 crystal interfaces

    • vmd_scripts/nup84_no-xray_density.tcl VMD script to calculate localization density for Nup84 with no crystal interfaces

    • vmd_scripts/ALPS_motif_density.tcl VMD script to calculate localization density for Nup84 at ALPS motif regions

    • chimera_scripts/nup84_density.cmd Chimera script to view all localization density files

  • output.1/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)

  • output.1/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 nup84 script:

with 3 crystal interfaces:

  • python nup84.isd.modeling.withXrayInterface.py & > nup84.isd.modeling.withXrayInterface.out (on a single processor; prepend mpirun -np 4 or similar if you built IMP with MPI support)
  • python nup84.merge.py
  • clustering_master_script_3-xray.sh
  • python nup84.analysis.py

with no crystal interfaces:

  • python nup84.isd.modeling.py &> nup84.isd.modeling.out
  • python nup84.merge.py
  • clustering_master_script_no-xray.sh
  • python nup84.analysis.py

Information

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

Date: September 2nd, 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: