IMOD

In the case of particle picking its usually sufficient to look at the translations in a viewer like IMOD. The following assumes that you have IMOD installed and its command line tools linked.

awk -F'\t' '
    BEGIN {OFS="\t"}
    NR==1 {next}
    {print 1, 1, $3, $2, $1}
' output.tsv > coordinates.tsv

point2model -inp coordinates.tsv -ou coordinates.mod -ci 10