Tutorial
Overview
Before you begin, please make sure that
- MUST is correctly installed;
- The path has been added to the enviroment variable ${PATH}. (Otherwise, you may run MUST with
${ROOTPATH}/must.)
Tutorial-1 Reconstruct from an aligned tilt-series stack
This section shows how to use MUST to reconstruct a tomogram from an aligned cryo-ET tilt-series.
- Step 0: Get the tutorial dataset
Download the tilt-series and the parameter file for this tutorial from here.
Decompress the zip file and enter the folder.
- Step 1: Generate the input micrograph list file
generate_input_list_cpp --output TS_43_bin4.list --input TS_43_bin4.ali --tilt TS_43.tlt --defocus defocus_file.txt
- Step 2.1: Reconstruct with WBP-like filter
must para_wbp.conf
- Step 2.2: Reconstruct with SIRT-like filter
must para_sirt.conf
- Step 2.3: Reconstruct with CTF deconvolution
must para_ctf.conf
- Step 2.4: Reconstruct with 3D-CTF correction
must para_3dctf.conf
- Step 3: Visualize the reconstructed tomogram
Note 1: CTF deconvolution shows better constrast for visualization than 3D-CTF correction, because 3D-CTF correction multiplies another CTF term to the tomogram. However, 3D-CTF-corrected tomograms may lead to higher-resolution structures for subsequent subtomogram averaging.
Note 2: If you try to reconstruct your own data of a larger size (e.g., an unbinned tomogram), it will take more time and require more GPU memory. If you run out of GPU memory, you can try to increase the parameter "N_block_rec" and "N_block_linear_combination" to divide the reconstruction process into more blocks.
Tutorial-2 Reconstruct from a raw tilt-series
This section shows how to use MUST to reconstruct a tomogram from a raw cryo-ET tilt-series with the alignment parameters from IMOD.
- Step 0: Get the tutorial dataset
Download the tilt-series and the parameter file for this tutorial from here.
Decompress the zip file and enter the folder.
- Step 1: Generate the input micrograph list file
generate_input_list_cpp --output TS_43.list --input TS_43.st --tilt TS_43.tlt --xf TS_43.xf --xtilt TS_43.xtilt --defocus defocus_file.txt
- Step 2.1: Reconstruct with WBP-like filter
must para_wbp.conf
- Step 2.2: Reconstruct with SIRT-like filter
must para_sirt.conf
- Step 2.3: Reconstruct with CTF deconvolution
must para_ctf.conf
- Step 2.4: Reconstruct with 3D-CTF correction
must para_3dctf.conf
- Step 3: Visualize the reconstructed tomogram
