Setup Ptolemy CLI shell script for Square Finding¶

The script needs to take two options

1. the output json file name without the extension
2. input mrc file path

• Within Leginon MosaicExternalScoreFinder instance defines, for each incoming gr image:

Here is an example of this shell script we call sq_finding.sh

#!/bin/sh -f
# Local runs
source /usr/local/anaconda3/etc/profile.d/conda.sh
conda activate /opt/condaenvs/ptolemy_env
# variable 1 is the outputname without json extension.
# variable 2 is the input mrc path
echo $1
echo $2
mrc_path=$2
python /home/your_name/packages/ptolemy/lowmag_cli.py -f json $2 > $1
conda deactivate
# mv the result to leginon session rawdata directory
mv $1 ${mrc_path%%rawdata/*}rawdata/$1.json
echo ${mrc_path%%rawdata/*}rawdata/$1.json

Test example, assuming you have /data/leginon/22feb28a/rawdata/22feb28a_00001gr.mrc, you can test ptolemy with

./sq_finding.sh test_1 /data/leginon/22feb28a/rawdata/22feb28a_00001gr.mrc

Output test_1.json should end up in /data/leginon/22feb28a/rawdata/