Tomogram reconstruction
Run the program
Please run MUST with a parameter file (described in detail later).
must para.conf
- Note: MUST by default uses all the GPUs on the computer. To specify the GPUs to use, please run the following command first (in bash shell format).
export CUDA_VISIBLE_DEVICES=<GPU IDs>
e.g., to use GPU #0 and #1,
export CUDA_VISIBLE_DEVICES=0,1
Parameter file
File convention
The parameter file is a text file in "<parameter name>=<parameter value>" style. Each line contains one parameter.
# This is a sample parameter file.
######## Basic parameters ########
path=./
input_micrograph_list=tomo_001.list
output_mrc=tomo_001.rec
h=500
pixel_size=5.4
j=10
######## Parameters for CTF correction ########
# skip_ctfcorrection=1
# ctf_deconvolve=0
# ctfcorrection_3d=0
# Cs=2.7
# voltage=300
# w=0.07
######## Advanced parameters ########
# output_style=1
# output_style_para=0
# tlt_offset=0.0
# it_sirt=100
# padding=2
# trimming=0
# bin=1
# lp=1.0
# h_offset=0
# h_padding=500
######## Parameters for blocking on GPU ########
# N_block_fft=2
# N_block_rec=2
# N_block_linear_combination=2
Please refer to conf/para_example.conf as an example, or you can download the example parameter file from here.
To write out a parameter file for reference, run
must --params_example <example parameter file>
Basic parameters
| Parameter name | Value for reference | Description |
|---|---|---|
| path | ./ | Work path, the folder for all input and output files |
| input_micrograph_list | tomo_001.list | Input micrograph list file name (Text file, see below for details) |
| output_mrc | tomo_001.rec | Output file name (MRC file) |
| h | 500 | Heigh of the reconstructed tomogram (in pixel) |
| pixel_size | 5.4 | Pixel size of the tilt-series（in Angstrom） |
| j | 10 | Number of threads (with OpenMP parallelization) |
Parameters for CTF correction
| Parameter name | Value for reference | Description |
|---|---|---|
| skip_ctfcorrection | 0/1 | Skip CTF correction (0-Don't skip; 1-Skip) |
| ctf_deconvolve | 0/1 | Correct CTF with deconvolution using a Wiener-like filter (0-Multiplication; 1-Deconvolution) |
| ctfcorrection_3d | 0/1 | Apply 3D-CTF correction (0-Don't apply; 1-Apply) (If set to 1, the parameter "skip_ctfcorrection" will be ignored) |
| Cs | 2.7 | Spherical aberration (in mm) |
| voltage | 300 | Acceleration voltage (in kV) |
| w | 0.07 | Amplitude contrast |
Advanced parameters
| Parameter name | Value for reference | Description |
|---|---|---|
| output_style | 0/1/2/3/4 | Output style (0 - Along the tilt axis in the 0-degree micrograph; 1 - Tilt axis = y-axis; 2 - Tilt axis = x-axis; 3 - Along the tilt axis of a specific micrograph; 4 - Along a specific tilt axis angle) |
| output_style_para | 0 | The parameter for the output style 3 or 4 (For 3 - The number of the micrograph (started from 0); For 4 - The tilt axis angle) |
| tlt_offset | 0.0 | Systematic tilt angle offset (in degree) |
| it_sirt | 100 | Number of iterations for SIRT-like filter (Particularly, 0 stands for WBP (turn off SIRT-like filter), 1 stands for BP (no weighting)) |
| padding | 2 | Padding factor of the micrographs before reconstruction (1 or 2 is recommended) |
| trimming | 0 | Trimming the micrograph to alleviate aliasing (0 - No trimming; 1 - Trimming) |
| bin | 1 | Binning factor |
| lp | 1.0 | Ratio of the cuf-off frequency with regard to the Nyquist frequency for lowpass filter (0~1, 1 means no filtering) |
| h_offset | 0 | Offset in height in reconstruction (in pixel) |
| h_padding | 500 | Padding in height direction (in pixel) (1 or 2 times of the reconstructed height is recommended. Typically, the higher this value, the higher the contrast of the reconstructed tomogram) |
Parameters for block dividing (in case of limited GPU memory)
| Parameter name | Value for reference | Description |
|---|---|---|
| N_block_fft | 2 | Number of blocks for dividing the tilt-series when doing FFT |
| N_block_rec | 2 | Number of blocks for dividing the reconstructed tomogram |
| N_block_linear_combination | 2 | Number of blocks for dividing the micrographs in linear combination |
Input micrograph list file
File convention
MUST v2.0.0 uses a micrograph list file as input. The input micrograph list file is a text file specifying the micrographs in the tilt-series. It contains 10 columns as following.
# Column 1 : Frame number@Micrograph name (Frame number starts from 0)
# Column 2 : Tilt angle (in degree)
# Column 3 : Tilt axis angle (in degree)
# Column 4 : Off-plane tilt angle of the tilt axis (x-tilt) (in degree)
# Column 5 : Translation in x-axis (in pixel)
# Column 6 : Translation in y-axis (in pixel)
# Column 7 : Defocus1 (in Angstrom)
# Column 8 : Defocus2 (in Angstrom)
# Column 9 : Astigmatism angle (in degree)
# Column 10 : Phase shift (in radian)
00@TS_43.st -59.78 85.20 0.00 -8.723 -31.449 26949.71 26898.25 57.16 0.00
01@TS_43.st -56.79 85.22 0.00 -16.130 -36.526 26735.87 26138.06 50.86 0.00
......
40@TS_43.st 60.51 85.36 0.00 20.409 59.958 26226.41 25569.01 50.96 0.00
Quick generation
Given the following files:
- The tilt-series stack (MRC file),
- The tilt angle file (text file, with one angle per line),
- Optional: The transform file (text file, the ".xf" file from IMOD, specifying the alignment parameters),
- Optional: The x-tilt file (text file, with one angle per line);
- Optional: The defocus file (text file, in CTFFIND4 style).
We provide a script to generate the input micrograph list file based on the above files.
generate_input_list --output <output micrograph list file name> --input <input raw tilt-series stack> --tilt <input tilt angle file> [--xf <input transform file (.xf from IMOD)>] [--xtilt <input x-tilt file>] [--defocus <input defocus file (in CTFFIND4 format)>]