Name

sxcter - CTF Estimation: Automated estimation of CTF parameters with error assessment.

Usage

usage in command line

sxcter.py input_image output_directory --wn=CTF_WINDOW_SIZE --apix=PIXEL_SIZE --Cs=CS --voltage=VOLTAGE --ac=AMP_CONTRAST --f_start=FREA_START --f_stop=FREQ_STOP --kboot=KBOOT --overlap_x=OVERLAP_X --overlap_y=OVERLAP_Y --edge_x=EDGE_X --edge_y=EDGE_Y --set_ctf_header --MPI --stack_mode --debug

Typical usage

sxcter exists in for both MPI and non-MPI versions.

Multi-Micrograph Mode - Processes a set of micrographs in a list text file or in a directory
Specify a micrograph list text file name (e.g. output of sxgui_unblur.py or sxgui_cter.py) and output directory as arguments. The file extension must be ".txt".

mpirun -np 16 sxcter.py mic_list.txt outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --MPI

Alternatively, specify a list of input micrographs and their corresponding coordinates using wild card (e.g. *). Running from the command line requires enclosing the string by single quotes (') or double quotes ("). sxgui.py will automatically adds single quotes to the string ('). BDB stacks can not be used as input.

mpirun -np 16 sxcter.py 'Micrographs/mic*.mrc' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --MPI

Single-Micrograph Mode - Processes a single micrograph
Only the micrograph name and output directory are used as arguments. BDB files can not be selected as input micrograph. Use single processor for this mode.

sxcter.py Micrographs/mic0.mrc outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0

Stack Mode - Processes a particle stack
Use option --stack_mode. The name of the particle stack and output directory are used as arguments. The --wn option will be ignored. This mode is Not supported by sxgui.py. Only implemented in the non-MPI version of sxcter.

sxcter.py bdb:stack outdir_cter --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --stack_mode

Input

input_image
Input micrographs: For the multi-micrograph mode, specify micrograph list text file name or file name pattern with a wild card (i.e. *). A particle stack can also be supplied with --stack_mode, but this mode is not supported by sxgui. (default required string)
wn
CTF window size [Pixels]: It should be slightly larger than particle box size. This is ignored in the stack mode. (default 512)
apix
Pixel size [A]: (default -1.0)
Cs
Microscope spherical aberration [mm]: (default 2.0)
voltage
Microscope voltage [kV]: (default 300.0)
ac
Amplitude contrast [%]: (default 10.0)
f_start
Starting frequency [1/A]: Lowest frequency to be considered in the CTF estimation. Determined automatically by default. (default -1.0)
f_stop
Stop frequency [1/A]: by Highest frequency to be considered in the CTF estimation. Determined automatically by default. (default -1.0)
  • The remaining parameters are optional.
  • kboot
    Number of estimates per micrograph: Used for error assessment. (default 16)
    overlap_x
    X overlap [%]: Overlap between the windows in the x direction. (default 50)
    overlap_y
    Y overlap [%]: Overlap between the windows in the y direction. (default 50)
    edge_x
    Edge x [Pixels]: Defines the edge of the tiling area in the x direction. Normally it does not need to be modified. (default 0)
    edge_y
    Edge y [Pixels]: Defines the edge of the tiling area in the y direction. Normally it does not need to be modified. (default 0)
    set_ctf_header
    Export parameters to header: Exports the estimated CTF parameters to the image header. Not supported in the particle stack mode. (default False)
    MPI
    Use MPI: (default False)
    stack_mode
    Use stack mode: Advanced option. Not supported by sxgui. (default False)
    debug
    Debug info: Prints debug information. (default False)

    Output

    output_directory
    Output directory: The CTF parameters (partres file), rotationally averaged power spectra (rotinf), and micrograph thumbnails (thumb files) will be written here. This directory will be created automatically and it must not exist previously. (default required string)

    After successful execution, sxcter will create in the output_directory:

    1. A CTF parameters file, written to partres.txt

    2. A list of rotationally averaged power spectra, written to pwrot/*_rotinf.txt.

    3. A collection of micrographs Thumbnails (512 x 512 pixels), written to micthumb/*_thumb.hdf.

    The CTF parameter file, partres.txt, contains 18 columns with the following information:

    Column

    Parameter

    1

    Image defocus [um]

    2

    Microscope spherical aberration [mm]

    3

    Microscope voltage [kV]

    4

    Pixel size [A]

    5

    B-factor [A^2]

    6

    Amplitude contrast [%]

    7

    Astigmatism amplitude [um]

    8

    Astigmatism angle [degrees]

    9

    Standard deviation of defocus [um]

    10

    Standard deviation of astigmatism amplitude [um]

    11

    Standard deviation of astigmatism angle [degrees]

    12

    Coefficient of variation of defocus [um]

    13

    Coefficient of variation of astigmatism amplitude [um]

    14

    Mean difference between the experimental rotational averages calculated with and without considering astigmatism. The subtraction is only performed at frequencies where the CTF model has a local minimum or maximum.

    15

    Frequency at which the signal drops by 50% due to estimated error of defocus alone [1/A]

    16

    Frequency at which the signal drops by 50% due to estimated error of defocus and astigmatism [1/A]

    17

    Frequency at which the CTF oscillation can no longer be modelled correctly due the pixel size of the image [1/A]

    18

    Micrograph name



    The rotationally averaged power spectra (rotinf.txt files) will be written to the pwrot directory. These files contain 6 columns with the following information:

    Column

    Parameter

    1

    Line number

    2

    Spatial frequency [1/A]

    3

    Experimental rotational average without considering astigmatism

    4

    Fitted rotational average without considering astigmatism

    5

    Experimental rotational average including astigmatism

    6

    Fitted rotational average including astigmatism

    Description

    'This is work in progress since 11/30/2013'

    NOTE: 2016/04/27 Toshio Moriya: IMPORTANT - Finished the major modification of I/O related arguments and options as well as formats of output files. Please update your installation if it is between 2015/12/27 - 2016/04/27.

    NOTE: 2016/03/17 Toshio Moriya: IMPORTANT - Started another major modification of I/O related arguments and options as well as formats of output files. This work is currently in progress.

    NOTE: 2015/12/27 Toshio Moriya: IMPORTANT - Major modification of I/O related arguments and options to simplified the interface.

    Author / Maintainer

    Pawel A. Penczek and Toshio Moriya

    Attachments

    80S ribosome determined using 35,198 projection images collected with a 300 kV Tecnai Polara (FEI) equipped with the K2 Summit DED camera. Resolution of the the large subunit is 3.84 Å (using FSC with 0.5 cut-off criterion). 80SK2.mrc.gz (Warning: file size is 21MB.)

    Keywords

    category 1
    APPLICATIONS

    Files

    sparx/bin/sxcter.py

    See also

    sxgui_cter, sxwindow

    Maturity

    beta
    works for author, often works for others.

    Bugs

    Fixed most of the bugs thus far.

    sxcter (last edited 2016-05-19 13:56:45 by penczek)