/cryosparc_utils2

CryoSPARC utility scripts utilizing cryosparc-tools library

Primary LanguagePythonMIT LicenseMIT

cryosparc_utils2

CryoSPARC utility scripts utilizing cryosparc-tools library

Installation

  1. Create a new virtual environment in Anaconda/Miniconda
conda create -n cryosparc_utils2 -c conda-forge python=3.10
conda activate cryosparc_utils2
  1. Clone this repository
git clone https://github.com/kttn8769/cryosparc_utils2.git
cd cryosparc_utils2
  1. Install dependencies and cryosparc_utils2
pip install .

Configuration

  • Create a file named .cryosparc_conf.json under your home directory.
{                                                         
    "license" : "CRYOSPARC LICENSE ID",   
    "host" : "CRYOSPARC MASTER HOSTNAME",                                 
    "base_port" : "CRYOSPARC BASE PORT NUMBER (by default 39000)",                                  
    "email" : "CRYOSPARC ACCOUNT EMAIL ADDRESS",        
    "password" : "CRYOSPARC ACCOUNT PASSWORD"                                
}                                                         

Usage

  • Activate the virtual environment
conda activate cryosparc_utils2
  • Check usage of each command with --help flag. For example,
cu2_compare_fsc --help

Examples

Compare FSC plot of different refinement jobs in a project

cu2_compare_fsc --project-uid P2 --job-uid-list J64 J66 J70 J72 --outfile fsc-p2-j64-j66-j70-j72.png

fsc-p2-j64-j66-j70-j72