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:

`2Y20_MC_1_FULL`

1-state modeling`2Y20_MC_2_FULL`

2-state modeling`2Y20_MC_2_FULL_90_PERCENT_DATA_1`

2-state modeling with 90% data jackknifing`2Y20_MC_2_FULL_90_PERCENT_DATA_2`

2-state modeling with 90% data jackknifing`2Y20_MC_2_FULL_95_PERCENT_DATA_1`

2-state modeling with 95% data jackknifing`2Y20_MC_2_FULL_95_PERCENT_DATA_2`

2-state modeling with 95% data jackknifing`2Y20_MC_3_FULL`

3-state modeling

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

`cd modeling/2Y20_MC_2_FULL`

`./HK_model_ENSEMBLE_REM.py`

(on a single processor; prepend`mpirun -np 4`

or similar if you built IMP with MPI support)

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.

*Testable*: Yes.

*Parallelizeable*: Yes

*Publications*:

- K. Molnar, M. Bonomi, R. Pellarin, G. Clinthorne, G. Gonzalez, S. Goldberg, M. Goulian, A. Sali, W. DeGrado. Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ, Structure 22, 1239-1251, 2014.