Warp

• Version: 2.0.0dev27 (2024-09-20)
• Test Source: Tutorial from Warp

Complete tutorial script:

# Start SBGrid Environment

source /programs/sbgrid.shrc
export WARP_X=2.0.0dev27

# download the gain reference
wget \
--timestamping \
--no-directories \
--directory-prefix ./ \
ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/gain_ref.mrc;

for i in 1 11 17 23 32;
do
    echo "======================================================"
    echo "================= Downloading TS_${i} ================"
    # download the mdoc file
    wget \
    --timestamping \
    --no-directories \
    --directory-prefix ./mdoc \
    ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/tiltseries/mdoc/TS_${i}.mrc.mdoc;

    # download the frames
    wget \
    --timestamping \
    --no-directories \
    --directory-prefix ./frames \
    ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/tiltseries/data/*-${i}_*.tif;
done

# Create Frame Series Settings File

WarpTools create_settings \
--folder_data frames \
--folder_processing warp_frameseries \
--output warp_frameseries.settings \
--extension "*.tif" \
--angpix 0.7894 \
--gain_path gain_ref.mrc \
--gain_flip_y \
--exposure 2.64

# Create Tilt Series Settings File
WarpTools create_settings \
--output warp_tiltseries.settings \
--folder_processing warp_tiltseries \
--folder_data tomostar \
--extension "*.tomostar" \
--angpix 0.7894 \
--gain_path gain_ref.mrc \
--gain_flip_y \
--exposure 2.64 \
--tomo_dimensions 4400x6000x1000


# Frame Series Motion and CTF Estimation
WarpTools fs_motion_and_ctf \
--settings warp_frameseries.settings \
--m_grid 1x1x3 \
--c_grid 2x2x1 \
--c_range_max 7 \
--c_defocus_max 8 \
--c_use_sum \
--out_averages \

# Plot Histograms of 2D Processing Metrics
WarpTools filter_quality --settings warp_frameseries.settings --histograms

# Import Tilt Series Metadata
WarpTools ts_import \
--mdocs mdoc \
--frameseries warp_frameseries \
--tilt_exposure 2.64 \
--min_intensity 0.3 \
--dont_invert \ 
--output tomostar

# Tilt Series Alignment in Etomo using Patch Tracking
WarpTools ts_etomo_patches \
--settings warp_tiltseries.settings \
--angpix 10 \
--patch_size 500 \ 
--initial_axis -85.6

# Defocus Handedness Check
WarpTools ts_defocus_hand \
--settings warp_tiltseries.settings \
--check

# Tilt Series CTF Estimation
WarpTools ts_ctf \
--settings warp_tiltseries.settings \
--range_high 7 \
--defocus_max 8

# Tomogram Reconstruction
WarpTools ts_reconstruct \
--settings warp_tiltseries.settings \
--angpix 10

# importing improved alignments for TS_1
WarpTools ts_import_alignments \
--settings warp_tiltseries.settings \
--alignments warp_tiltseries/tiltstack/TS_1 \
--alignment_angpix 10

# Template Matching with a Template from the EMDB
WarpTools ts_template_match \
--settings warp_tiltseries.settings \
--tomo_angpix 10 \
--subdivisions 3 \
--template_emdb 15854 \
--template_diameter 130 \
--symmetry O \
--whiten \
--check_hand 2

# Select Peaks from Template Matching Results
WarpTools threshold_picks \
--settings warp_tiltseries.settings \
--in_suffix 15854 \
--out_suffix clean \
--minimum 6

# Export 2D particle series
WarpTools ts_export_particles \
--settings warp_tiltseries.settings \
--input_directory warp_tiltseries/matching \
--input_pattern "*15854_clean.star" \
--normalized_coords \
--output_star relion/matching.star \
--output_angpix 4 \
--box 64 \
--diameter 130 \
--relative_output_paths \
--2d