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Spindle Pole Body core

Modeling of the yeast spindle pole body (SPB) 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 scipy matplotlib numpy 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 scipy matplotlib numpy

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

module load imp python/scipy python/matplotlib python/numpy
Tags EM in-vivo FRET SAXS yeast two-hybrid

DOI

This repository pertains to the molecular architecture of the yeast spindle pole body (SPB), the structural and functional equivalent of the metazoan centrosome. Data from in vivo FRET and yeast two-hybrid, along with SAXS, X-ray crystallography, and electron microscopy were integrated by a Bayesian structure modeling approach.

The repository contains input data, scripts for modeling and results including bead models and localization probability density maps. It uses IMP (Integrative Modeling Platform).

Prerequisites for running the code

Note that the SPB code is almost fully written in C++ and uses native IMP, unlike most other recent integrative modeling projects that use PMI. The SPB modeling relies on the IMP.spb module, which is included with IMP version 2.9.0 or later. The IMP code must be compiled with MPI support so that replica exchange can be used.

Folder structure:

  1. inputs : contains all the input data used for modeling such as PDB files, FRET experimental values, and so on.
  2. config_files: contains the config files for each step of modeling: these have the parameters used for each step.
  3. results : contains the results of initial and final modeling runs, showing the models and localization densities of various clusters, along with the fit to FRET data.
  4. scripts : configuration files, bash scripts and sample scripts to run jobs on the cluster are provided, that call the SPB C++ code.

Information

Author(s): Shruthi Viswanath, Massimiliano Bonomi

Date: June 6th, 2017

License: CC BY-SA 4.0 This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.

Last known good IMP version: build info build info

Testable: Yes.

Parallelizeable: Yes

Publications: