To use this environment,

1. Modify configure-env to add cisTEM to path
2. Place micrographs into micrographs/
3. Modify configure-metadata to match the parameters of these micrographs
4. Estimate micrograph CTFs with the command bash estimate_ctfs.sh. Results are written to ctfs/
5. Place template(s) to be used for template matching into templates/. If multiple templates in templates/ are present, each template will be run on each micrograph in micrographs/
6. Run 2DTM with the command bash match_templates.sh. Results are written to output/

Note: the estimate_ctfs.sh / match_templates.sh scripts either call the scripts/estimate_ctf.sh or scripts/estimate_ctf.slurm / scripts/match_template.sh or scripts/match_template.slurm. Edit these files to choose whether or not to run the scripts in bash or to queue with sbatch. If using sbatch, modify the default slurm parameters in each .slurm script.