examples/warp.md
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+# **Warp**
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+- **Version:** 2.0.0dev27 (2024-09-20)
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+- **Test Source:** [Tutorial from Warp](https://warpem.github.io/warp/user_guide/warptools/quick_start_warptools_tilt_series/#create-warp-settings-files)
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+
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+
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+# Complete tutorial script:
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+
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+```shell
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+
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+# Start SBGrid Environment
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+
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+source /programs/sbgrid.shrc
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+export WARP_X=2.0.0dev27
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+
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+# download the gain reference
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+wget \
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+--timestamping \
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+--no-directories \
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+--directory-prefix ./ \
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+ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/gain_ref.mrc;
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+
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+for i in 1 11 17 23 32;
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+do
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+ echo "======================================================"
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+ echo "================= Downloading TS_${i} ================"
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+ # download the mdoc file
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+ wget \
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+ --timestamping \
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+ --no-directories \
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+ --directory-prefix ./mdoc \
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+ ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/tiltseries/mdoc/TS_${i}.mrc.mdoc;
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+
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+ # download the frames
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+ wget \
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+ --timestamping \
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+ --no-directories \
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+ --directory-prefix ./frames \
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+ ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/tiltseries/data/*-${i}_*.tif;
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+done
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+
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+# Create Frame Series Settings File
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+
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+WarpTools create_settings \
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+--folder_data frames \
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+--folder_processing warp_frameseries \
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+--output warp_frameseries.settings \
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+--extension "*.tif" \
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+--angpix 0.7894 \
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+--gain_path gain_ref.mrc \
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+--gain_flip_y \
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+--exposure 2.64
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+
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+# Create Tilt Series Settings File
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+WarpTools create_settings \
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+--output warp_tiltseries.settings \
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+--folder_processing warp_tiltseries \
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+--folder_data tomostar \
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+--extension "*.tomostar" \
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+--angpix 0.7894 \
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+--gain_path gain_ref.mrc \
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+--gain_flip_y \
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+--exposure 2.64 \
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+--tomo_dimensions 4400x6000x1000
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+
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+
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+# Frame Series Motion and CTF Estimation
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+WarpTools fs_motion_and_ctf \
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+--settings warp_frameseries.settings \
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+--m_grid 1x1x3 \
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+--c_grid 2x2x1 \
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+--c_range_max 7 \
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+--c_defocus_max 8 \
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+--c_use_sum \
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+--out_averages \
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+
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+# Plot Histograms of 2D Processing Metrics
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+WarpTools filter_quality --settings warp_frameseries.settings --histograms
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+
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+# Import Tilt Series Metadata
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+WarpTools ts_import \
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+--mdocs mdoc \
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+--frameseries warp_frameseries \
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+--tilt_exposure 2.64 \
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+--min_intensity 0.3 \
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+--dont_invert \
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+--output tomostar
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+
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+# Tilt Series Alignment in Etomo using Patch Tracking
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+WarpTools ts_etomo_patches \
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+--settings warp_tiltseries.settings \
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+--angpix 10 \
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+--patch_size 500 \
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+--initial_axis -85.6
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+
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+# Defocus Handedness Check
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+WarpTools ts_defocus_hand \
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+--settings warp_tiltseries.settings \
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+--check
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+
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+# Tilt Series CTF Estimation
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+WarpTools ts_ctf \
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+--settings warp_tiltseries.settings \
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+--range_high 7 \
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+--defocus_max 8
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+
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+# Tomogram Reconstruction
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+WarpTools ts_reconstruct \
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+--settings warp_tiltseries.settings \
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+--angpix 10
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+
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+# importing improved alignments for TS_1
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+WarpTools ts_import_alignments \
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+--settings warp_tiltseries.settings \
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+--alignments warp_tiltseries/tiltstack/TS_1 \
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+--alignment_angpix 10
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+
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+# Template Matching with a Template from the EMDB
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+WarpTools ts_template_match \
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+--settings warp_tiltseries.settings \
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+--tomo_angpix 10 \
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+--subdivisions 3 \
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+--template_emdb 15854 \
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+--template_diameter 130 \
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+--symmetry O \
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+--whiten \
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+--check_hand 2
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+
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+# Select Peaks from Template Matching Results
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+WarpTools threshold_picks \
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+--settings warp_tiltseries.settings \
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+--in_suffix 15854 \
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+--out_suffix clean \
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+--minimum 6
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+
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+# Export 2D particle series
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+WarpTools ts_export_particles \
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+--settings warp_tiltseries.settings \
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+--input_directory warp_tiltseries/matching \
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+--input_pattern "*15854_clean.star" \
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+--normalized_coords \
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+--output_star relion/matching.star \
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+--output_angpix 4 \
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+--box 64 \
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+--diameter 130 \
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+--relative_output_paths \
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+--2d
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+
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+
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+```