Cryo-Tomography Data Processing’s Manual

This is my personal notebook for data processing - workflow ranges from data acquisition to subtomogram averaging and modeling.

There are many different software packages used for data processing.

The following is the current workflow to subtomogram averaging:

Guide for Software and Installation

• Home
• Installation miniconda
  • Configuration conda environment
    • 1. Download & Install miniconda3
    • 2. Create environment with name and specific python version:
    • 3. Add program into PATH variable
    • 4. Configuration of multiple GCC and G++
• Installation IMOD software
  • Linux system - Ubuntu 22.04LTS
    • 1. Download & Install imod
    • 2. Install PEET
• Installation emClarity for subtomogram averaging
  • Linux system - Ubuntu 22.04LTS
    • 1. Download & Install matlab runtime
      • To configure matlab runtime path:
    • 2. Download latest emclarity version
    • 3. Make test run to check installation
• Tomogram Reconstruction using eTomo
  • IMOD version: 4.12.30 & Ubuntu 22.04 LTS
    • 1. Prepare tilt-series for emClarity workflow
    • 2. Initiate eTomo
    • 3. Make test run to check installation

Subtomogram averaging workflow

Help

Useful script is at my repository on GitHub: https://github.com/hongzhan2015/cryoet