([first-ring],[last-ring],[search-range],[step-size],[max-wait]) ; USAGE: ./spider spi/dat @realign-pubsub 1 > log1.txt & ; ----------------------- Parameters ----------------------- [first-ring] = 5 ; first ring, for 2D alignment [last-ring] = -1 ; last ring, for 2D alignment (-1==calculated later) [search-range] = 10 ; translation search range, for 2D alignment [step-size] = 2 ; translation step size, for 2D alignment [max-wait] = 600 ; maximum headstart in seconds for copying stacks before next defocus group starts ; ------------------------- Inputs ------------------------- fr g [df_group_list]../Reconstruction/sel_group_cclim_sorted ; list of defocus groups fr g [params]../params ; parameter doc file, only needed if last ring for AP SH is unspecified fr g [selection]../Reconstruction/sel_particles_{***[grp-num]} ; selection file, for each defocus group fr g [ref_1_dir]../Alignment1 ; input-output directory for reference #1 fr g [ref_2_dir]../Alignment2 ; input-output directory for reference #2 fr g [reference_angles_doc][ref_2_dir]/refangles ; Euler angles of the reference-projections fr g [unaligned_images][ref_2_dir]/data{***[grp-num]}@ ; unaligned particle stacks fr g [align_doc]align_01_{***[grp-num]} ; alignment docs, in both REF_1_DIR and REF_2_DIR fr g [ref_proj_stem]projs/prj_{***[grp-num]} ; reference projections, in both REF_1_DIR and REF_2_DIR fr g [ref_proj_template][ref_proj_stem]@***** ; reference projections, in both REF_1_DIR and REF_2_DIR ; ------------------------ Outputs ------------------------ fr g [realigned_align_doc_1][ref_1_dir]/[align_doc]_realigned ; realignment doc file, reference 1 fr g [realigned_align_doc_2][ref_2_dir]/[align_doc]_realigned ; realignment doc file, reference 2 fr g [dummy_wait_file]jnk_scwait*** ; dummy file created when defocus-group done copying fr g [finished_flag]flag-realign-done_{***[grp-num]} ; dummy file created when defocus-group done with everything ; -------------------- END BATCH HEADER -------------------- re