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γTuSC-Spc110 Complex

Integrative model of the γTuSC-Spc110 complex

crossWarning: these files have not yet been verified to work with the latest version of IMP. We will update this page when they have been. The files are also available at GitHub.
Additional software needed to use these files: IMP scikit-learn 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 scikit-learn matplotlib numpy

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

module load Sali
module load imp python3/scikit python3/matplotlib python3/numpy
Tags chemical crosslinks cryo-EM X-ray

Integrative model of the γTuSC-Spc110 complex

This repository pertains to the integrative model of the γTuSC-Spc110 complex based on data from cryo-EM, chemical crosslinking, and X-ray crystallography.

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

Folder structure:

  1. inputs : contains all the input data used for modeling such as PDB files and crosslink files.
  2. scripts : scripts to prep input files, perform sampling, and analysis are provided.
  3. results : contains the models and localization densities of the top cluster.
  4. test : scripts for testing the sampling

Protocol:

Simulations

There are three independent simulations:

  1. Modeling of one copy of γTuSC bound to Spc110 dimer : gtusc_spc110dimer or dimer
  2. Modeling of one copy of γTuSC bound to Spc110 monomer : gtusc_spc110monomer or monomer
  3. Modeling of two copies of laterally associated γTuSC bound to one Spc110 dimer each : lateral_gtusc_spc110tetramer or tetramer

Sampling

To run the sampling, run modeling scripts like this

mpirun -np 6 $IMP python scripts/sample/sample_SCRIPTNAME.py prod

where $IMP is the setup script corresponding to the IMP installation directory (omit for binary installation)
and SCRIPTNAME can be, for example, gtusc_110dimer_1-220GCN4_nointra110xlinks for the dimer simulations.

50 production runs were performed in the above manner for each of the simulations.

Analysis

Good scoring models were selected using imp-sampcon as shown in scripts/analysis/get_gsms.sh

Sampling exhaustiveness tests were performed using imp-sampcon as shown in scripts/analysis/sampcon.sh

Crosslink violations were analyzed using scripts/analysis/get_xlink_violations_gtuscSpc110.py

Results

For each of the simulations, the following files are in the results directory

Information

Author(s): Shruthi Viswanath

Date: Dec 2nd, 2020

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: