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γTuSC-Spc110 Complex

Integrative model of the γTuSC-Spc110 complex PDB-Dev

tickVerified to work with the latest stable IMP release (2.15.0). 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

DOI

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: