IMP_Toolbox

Note

If you can not find any of the scripts you have previously used from IMP_Toolbox in the main branch , please check in the archive branch.

• A toolbox to aid integrative modeling with IMP.

• See Modeling with IMP for helpful tips while starting.

Pre-requisites

• Conda or Miniconda (https://www.anaconda.com/docs/getting-started/miniconda/install/linux-install)
• Fedora OS

Installation

• To use IMP_Toolbox, clone this repository

  git clone https://github.com/isblab/IMP_Toolbox.git

• Add the path to ~/.bash_profile. You can then use it as a module.

  # replace the path and add it at the end of ~/.bash_profile
  export PYTHONPATH=/path/to/IMP_Toolbox:$PYTHONPATH

• If you want to install IMP, follow the instructions given in IMP installation and activate the conda environment.

  conda activate imp_omg

• Alternatively, if you only want to use IMP_Toolbox without installing IMP, create a new conda environment. You need Python >=3.12.

  conda create -n imp_toolbox python=3.12
  conda activate imp_toolbox

• Install the required packages from requirements.txt.

  pip install -r requirements.txt

Optional

• If you plan to use sequence module, you need to install EMBOSS package as follows:

  sudo dnf install EMBOSS

• If you plan to use structure.burial, you need to download DSSP.

  sudo dnf install dssp

• If you plan to use structure.burial.get_burial_info with include_residue_depth set to True, you also need MSMS installed.

IMP Installation

• Go to IMP_installation directory

• Run the following command in terminal. (change the installation path and conda environment)

  bash install_imp_conda.sh \
    -e imp_omg \
    -i ~/IMP_OMG \
    -s tarball \
    -I 2.24.0 \
    -c 16 \
    -P 3.12

• Use -h flag to see more details.

Additional Information

License: GPLv3

Testable: Yes