alisterburt / emclarity_setup

Takes a set of tilt series aligned in IMOD and prepares the files necessary for emClarity

emClarity_setup.py

Simple user-friendly script for setting up an emClarity project from a set of IMOD alignments

USAGE: emClarity_setup.py -i <IMOD_BASE_DIR> -o <EMCLARITY_PROJECT_DIR>

Argument	Input	Explanation
-i	<IMOD_BASE_DIR>	Directory containing all tilt series reconstructed in IMOD
-o	<EMCLARITY_PROJECT_DIR>	emClarity project directory, necessary files will be copied here

Example:

Want to set up an emClarity project tilt-series & IMOD alignments found in subdirectories of /home/user/tilt_series and put all necessary files in /home/user/emClarity_proj...

python emClarity_setup.py -i /home/user/tilt_series -o /home/user/emClarity_proj

Requirements:

IMOD programs must be on the path (one step involves conversion of model file to .txt file containing model coordinates