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.,
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_mrc=tomo_001.ali
input_tlt=tomo_001.tlt
output_mrc=tomo_001.rec
h=500
psi=0.0
pixel_size=5.4
j=10
######## Parameters for CTF correction ########
# skip_ctfcorrection=1
# ctf_deconvolve=0
# ctfcorrection_3d=0
# defocus_file=defocus_file.txt
# Cs=2.7
# voltage=300
# w=0.07
######## Advanced parameters ########
# tlt_offset=0.0
# psi_x=0.0
# it_sirt=100
# padding=2
# lp=1.0
# h_offset=0
# h_padding=500
# dose_weighting=0
# dose_file=tomo_001.dose
######## 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_mrc | tomo_001.ali | Input tilt-series (MRC file, after alignment) |
| output_mrc | tomo_001.rec | Output reconstructed tomogram (MRC file) |
| input_tlt | tomo_001.tlt | Tilt angles of the input tilt-series (in degree, one angle per line, corresponding to the micrographs in the tilt-series in the same order) |
| psi | 0.0 | Tilt axis angle (in degree, rotate clockwise to make the tilt axis align with the y-axis, 0 if the tilt axis is the y-axis) |
| 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 (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" and "ctf_deconvolve" will be ignored) |
| Cs | 2.7 | Spherical aberration (in mm) |
| voltage | 300 | Acceleration voltage (in kV) |
| w | 0.07 | Amplitude contrast |
| defocus_file | defocus_file.txt | Input file for the defocus parameters of the tilt-series (in CTFFIND4 style) |
Advanced parameters
| Parameter name | Value for reference | Description |
|---|---|---|
| psi_x | 0.0 | Rotation around the x-axis (x-tilt) after reconstruction (in degree) |
| 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-like filter (turn off SIRT-like filter)) |
| padding | 2 | Padding factor of the micrographs before reconstruction (1 or 2 is recommended) |
| 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, 2, or 4 times of the reconstructed height is recommended. Typically, the higher this value, the higher the contrast of the reconstructed tomogram) |
| dose_weighting | 0/1 | Apply dose weighting (0-Don't apply; 1-Apply) |
| dose_file | tomo_001.dose | A text file with the accumulated dose of each micrograph in the input tilt-series (One number per line, in $e^-/\rm{\AA}^2$, corresponding to the micrographs in the tilt-series in the same order) |
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 |