Installation emClarity for subtomogram averaging

Linux system - Ubuntu 22.04LTS

To get the latest emClarity github, please visit emClarity for more information.

Note

It is possible to rebuild emClarity from its source code. But it is pretty difficult to do.

emClarity runs on GPUs, and both workstation with Titan RTX and GPU server equipped with A100 will do the job. Attention for matlab runtime version.

You also need to make sure IMOD and Chimera on the PATH so that emClarity can find them.

Make sure CUDA is in the PATH also.

1. Download & Install matlab runtime

Require matlab runtime v2021a.

To install matlab runtime:

wget https://ssd.mathworks.com/supportfiles/downloads/R2021a/Release/8/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R2021a_Update_8_glnxa64.zip
mkdir matlab_runtime_install
unzip glnxa64/MATLAB_Runtime_R2021a_Update_8_glnxa64.zip -d ./matlab_runtime_install
sudo ./install -agreeToLicense yes

To configure matlab runtime path:

OS system	Env Var	Dir
Windows OS	PATH	<MATLAB_RUNTIME_INSTALL_DIR>runtime<arch>
Linux OS	LD_LIBRARY_PATH	<MATLAB_RUNTIME_INSTALL_DIR>/runtime/glnxa64 <MATLAB_RUNTIME_INSTALL_DIR>/bin/glnxa64 <MATLAB_RUNTIME_INSTALL_DIR>/sys/os/glnxa64 <MATLAB_RUNTIME_INSTALL_DIR>/extern/bin/glnxa64
Mac OS	DLD_LIBRARY_PATH	<MATLAB_RUNTIME_INSTALL_DIR>/runtime/maci64 <MATLAB_RUNTIME_INSTALL_DIR>/bin/maci64 <MATLAB_RUNTIME_INSTALL_DIR>/sys/os/maci64 <MATLAB_RUNTIME_INSTALL_DIR>/extern/bin/maci64

2. Download latest emclarity version

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