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.
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_FULL1-state modeling2Y20_MC_2_FULL2-state modeling2Y20_MC_2_FULL_90_PERCENT_DATA_12-state modeling with 90% data jackknifing2Y20_MC_2_FULL_90_PERCENT_DATA_22-state modeling with 90% data jackknifing2Y20_MC_2_FULL_95_PERCENT_DATA_12-state modeling with 95% data jackknifing2Y20_MC_2_FULL_95_PERCENT_DATA_22-state modeling with 95% data jackknifing2Y20_MC_3_FULL3-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; prependmpirun -np 4or 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.
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:
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.