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Exosome modeling

Modeling exosome complexes from cross-link MS data PubMed logo PDB-Dev

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 scikit-learn matplotlib 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 scikit-learn matplotlib

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

module load imp python/scikit python/matplotlib
Tags chemical crosslinks endogenous complex PMI X-ray

DOI

This repository contains the modeling scripts, the ensemble of models, and the results of the analysis for the modeling of the S.cerevisiae exosome complex (named exo10, comprising of Rrp40, Rrp4, Csl4, Rrp45, Rrp46, Rrp42, Rrp43, Mtr3, Ski6 and Rrp44), in presence of Ski7 (exo10+Ski7 below) or Rrp6 (exo10+Rrp6 below) proteins. The modeling is performed based on cross-link Mass-Spectrometry data, crystallographic structures, and comparative models.

Displaying the models

To display the models and the localization densities using UCSF Chimera access ./Rrp6.analysis/kmeans_weight_500_2/cluster.1/ or ./Ski7.analysis/kmeans_weight_500_2/cluster.1/ and run chimera chimera.session.py

Running the modeling script:

For more details on how to install IMP, run the modeling scripts and analyse the results using IMP and IMP.pmi see the IMP tutorial.

To run the modeling script, access: sampling/modeling and then run with:

python modeling.py

We recommend building IMP with MPI support, then running the modeling script with 64 replicas by prepending mpirun -np 64 to the above command.

Content of the directories:

modeling-scripts_Rrp6.1 modeling scripts and output modeling data for exo10+Rrp6 complex (first calculation)

modeling-scripts_Rrp6.2 modeling scripts and output modeling data for exo10+Rrp6 complex (second calculation)

modeling-scripts_Ski7.1 modeling scripts and output modeling data for exo10+Ski7 complex (first calculation)

modeling-scripts_Ski7.2 modeling scripts and output modeling data for exo10+Ski7 complex (second calculation)

README.md this readme file

Rrp6.analysis analysis for exo10+Rrp6 complex

Ski7.analysis analysis for exo10+Ski7 complex

data cross-linking data, fasta files, pdbs needed for the calculation

metadata files needed for the repository

test files needed to run tests

Content of the modeling-scripts* directories:

exosome.modeling.py modeling script (see above)

job.sh computer-cluster submission script (for UCSF QB3 cluster)

output all output data

output/pdbs best scoring 500 pdb files

output/rmfs rmf files for each replica

output/stat.*.out stat files containing modeling data (the index is the index of replica). To be read using the python program IMP_source/modules/pmi/pyext/src/process_output.py

output/stat_replica.*.out stat files containing replica exchange data. To be read using IMP_source/modules/pmi/pyext/src/process_output.py

Content of the *.analysis directories:

clustering.py: clustering script

kmeans_weight_500_2: the set of 500 best scoring models collected in two clusters

precision_rmsf.py: calculate the precision of clusters, their mutual distance and the RMSF

XL_table.py: calculate the contact map and the cross-link map

cluster.0: data for cluster 1

cluster.1: data for cluster 2

precision.0.0.out,precision.0.1.out,... : files containing the precision of a cluster (i.e., the files with the same indexes, precision.i.i.out, e.g., precision.0.0.out) and the files containing the distance between the clusters (i.e., files with different indexes, precision.i.j.out).

Content of the *.analysis/cluster.* directories

0.pdb,1.pdb,2.pdb....: the pdb files of the solutions

0.rmf3,1.rmf3,2.rmf3,...: the rmf files of the solution (can be opened with UCSF Chimera)

rmsf.Ski7.dat,rmsf.Rrp6.dat,...: text file of the RMSF analysis

rmsf.Ski7.pdf,rmsf.Rrp6.pdf,...: pdf file of the RMSF analysis

chimera_session.py: Chimera session file to display the localization densities

stat.out: stat file containing all relevant information on the score, etc.

XL_table_tail.pdf: pdf file of the cross-link map for the complex

Information

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: