Sparse Pattern INDexing toolkit

Authors & Contributors:

• Chufeng Li(Proposer) [email protected]
• Xuanxuan Li(Developer) [email protected]
• Richard Kirian [email protected]
• Nadia Zatsepin [email protected]
• John Spence [email protected]
• Haiguang Liu [email protected]

Installation

First, install some necessary tools. For CentOS users, just use the following command,

sudo yum install -y git wget bzip2

Then download SPIND package,

git clone https://github.com/LiuLab-CSRC/indexing.git

Install CrystFEL-SPIND

To integrate SPIND into CrystFEL, we add SPIND module to CrystFEL-0.6.2. See detailed installation instructions here.

Install SPIND

SPIND is implemented using Python, you do not have to do standard configure, make, make install, just install necessary dependencies.

SPIND package has the following dependencies,

• numpy
• scipy
• h5py
• mpi4py
• yaml
• tqdm

To make life easier, anaconda is highly recommended for Python-related library management.

Download anaconda for Python2.7 by

wget https://repo.continuum.io/archive/Anaconda2-5.0.1-Linux-x86_64.sh

Install anaconda,

bash Anaconda2-5.0.1-Linux-x86_64.sh

Accept the license then wait minutes for installation.

After the installation, make the installer prepend anaconda location to PATH in your .bashrc file.

Then source ~/.bashrc.

Finally, install SPIND dependencies using

conda install mpi4py yaml docopt tqdm

Installation is done! Congratulations!

Usage

Visit https://liulab-csrc.github.io/SPIND/ for usage manual.

Todo

• resolution shell
• SFX tutorial
• integrate SPIND in official CrystFEL
• multi-crystal diffraction tutorial

Citation for SPIND

@article{li2019spind,
  title={SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data},
  author={Li, Chufeng and Li, Xuanxuan and Kirian, Richard and Spence, John CH and Liu, Haiguang and Zatsepin, Nadia A},
  journal={IUCrJ},
  volume={6},
  number={1},
  year={2019},
  publisher={International Union of Crystallography}
}