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PhoQ

Multi-state modeling of the PhoQ two-component system PubMed logo

tickVerified to work with the latest stable IMP release (2.9.0). The files are also available at GitHub.
Additional software needed to use these files: IMP biopython install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp biopython

UCSF logo To set up the environment on the UCSF QB3 cluster to run this system, run:

module load imp
Tags cysteine crosslinks multi-state

DOI

This directory contains the input data, protocols and output model for the modeling of the PhoQ homodimer, using cysteine crosslinking and multi-state Bayesian modeling in IMP.

Directories:

solution_ensemble: all the 2-state models within the same cluster of similar structures. Each model is made of two structures, labeled by number 1 and 2.

localization_densities: all the calculated localization densities, for given domains, and for the two states.

ucsf_chimera_files: files used to generate the figures in the paper.

modeling: scripts for modeling the system:

To run a modeling script, just change into its directory and run it from the command line, e.g.

Two output files will be produced: a log file containing statistics, and a trajectory of model structures in RMF format. The latter can be viewed in UCSF Chimera.

Information

Author(s): Max Bonomi, Riccardo Pellarin, Ben Webb

Date: March 18th, 2015

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: Yes

Publications: