Tomogram Reconstruction using eTomo

IMOD version: 4.12.30 & Ubuntu 22.04 LTS

Note

Prepare tilt series into individual directory, which can be helpful for afterwards processing.

In SerialEM, saving .mdoc file for each tilt is very helpful, if not, using script to reorder tilt series from -54 to 54.

The following note using .mrc file withouth .mdoc.

Name tilt-series as TS_XX.st

1. Prepare tilt-series for emClarity workflow

Making image stacks:

newstack ??*.mrc TS_27/TS_27.st

2. Initiate eTomo

Start eTomo:

etomo

Go to emClarity GitHub and in the Wiki page, download by clicking the latest version v1.6.1: https://github.com/StochasticAnalytics/emClarity/wiki

After download, editing the emclarity_1.6.0_v21a file to point out the matlab runtime path:

MCR_BASH=/usr/local/MATLAB/MATLAB_Runtime/v910/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v910/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v910/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v910/extern/bin/glnxa64

export emClarity_ROOT=/home/hzhan/emClarity_1.6.0/emClarity_1.6.1.0
export LD_LIBRARY_PATH=${emClarity_ROOT}/lib:${MCR_BASH}:${LD_LIBRARY_PATH}

Creating a emClarity alias so that you can call emClarity easily:

#!/bin/bash
export PATH="/home/hzhan/emClarity_1.6.0/emClarity_1.6.1.0/bin:$PATH"
alias emClarity='/home/hzhan/emClarity_1.6.0/emClarity_1.6.1.0/bin/emClarity_1_6_1_0_v21a'

3. Make test run to check installation

emClarity check

If you want to check detailed manual created by Thomas Frosio, here is the link to his github: https://github.com/ffyr2w/emClarity-tutorial