Micctfdetermine¶
Program to determine CTF parameters from a set of micrographs using CTFFIND and CTFTILT (Mindell and Grigorieff JSB, 2003)
Input: Micrographs
Output: Diagnostic plot pattern
Parameters¶
Parameter |
Example (default) |
Description |
|---|---|---|
Micrographs |
cs_scan034.tif |
Input micrographs: accepted file formats (tif, .mrc, .mrcs, .spi, .hdf, .img, .hed). |
Diagnostic plot pattern |
micctfdetermine_diag.pdf |
If single input micrograph: name of diagnostic plot file. In case of multiple input micrographs suffix to be attached to corresponding input micrograph. Output: accepted file formats (pdf, .png, .bmp, .emf, .eps, .gif, .jpeg, .jpg, .ps, .raw, .rgba, .svg, .svgz, .tif, .tiff). |
Spherical aberration |
2.0 |
Spherical aberration - property of your electron microscope (accepted values min=0, max=10). |
Electron voltage in kV |
200 |
Electron beam voltage of your microscope in kV (accepted values min=0, max=1000). |
Pixel size in Angstrom |
1.163 |
Pixel size is an imaging parameter (accepted values min=0.001, max=100). |
Sample parameter file¶
You may run the program in the command line by providing the parameters via a text file:
micctfdetermine --f parameterfile.txt
Where the format of the parameters is:
Micrographs = cs_scan034.tif
Diagnostic plot pattern = micctfdetermine_diag.pdf
Spherical aberration = 2.0
Electron voltage in kV = 200
Pixel size in Angstrom = 1.163
Additional parameters (intermediate level)¶
Parameter |
Example (default) |
Description |
|---|---|---|
Range of defocus in Angstrom |
(10000, 45000) |
Images were taken at this defocus range in Angstrom. Positive values for underfocus. FEI microscopes tend to have an offset to the theoretical values of 6000 Angstrom (accepted values min=0, max=100000). |
Resolution search range in Angstrom |
(30.0, 6.0) |
Maximum and minimum resolution rings to be included in CTF determination (accepted values min=1, max=100). |
Binning option |
True |
Micrograph is reduced in size by binning. |
Binning factor |
2 |
Micrograph is reduced in size by binning factor (accepted values min=1, max=20). |
MPI option |
True |
OpenMPI installed (mpirun). |
Number of CPUs |
2 |
Number of processors to be used. Maximum number corresponds directly to number of input scans, i.e. no gain in performance if single input micrograph chosen (accepted values min=1, max=300). |
Temporary directory |
/tmp |
Temporary directory should have fast read and write access. |
Sample parameter file (intermediate level)¶
You may run the program in the command line by providing the parameters via a text file:
micctfdetermine --f parameterfile.txt
Where the format of the parameters is:
Micrographs = cs_scan034.tif
Diagnostic plot pattern = micctfdetermine_diag.pdf
Spherical aberration = 2.0
Electron voltage in kV = 200
Pixel size in Angstrom = 1.163
Range of defocus in Angstrom = (10000, 45000)
Resolution search range in Angstrom = (30.0, 6.0)
Binning option = True
Binning factor = 2
MPI option = True
Number of CPUs = 2
Temporary directory = /tmp
Additional parameters (expert level)¶
Parameter |
Example (default) |
Description |
|---|---|---|
Spring database option |
False |
If checked will read previous spring.db (Sqlite-compatible database) otherwise will create new one. |
spring.db file |
spring.db |
Program requires a previously generated spring.db and writes an updated spring.db database in the working directory. |
Continue spring.db option |
False |
Continue spring.db without re-computing previously determined CTF of micrographs. Do not tick in case you want to update the Ctf results of the micrographs in the provided database. |
Amplitude contrast |
0.1 |
Amplitude contrast (between 0 and 1). For cryo data ranges from 0.07 to 0.14 and negative stain from 0.1 - 0.4 have been reported (accepted values min=0, max=1). |
Defocus search step size |
300 |
Choose defocus search step size. Smaller step size will result in slower search (accepted values min=0, max=5000). |
Astigmatism search restraint in Angstrom |
2000 |
Astigmatism in Angstrom. This is useful in case Thon rings are not well visible (accepted values min=0, max=50000). |
Tile size power spectrum in Angstrom |
600 |
Tile size to be used for analysis. It will be internally converted to nearest power-of-two pixel dimensions (accepted values min=1, max=10000). |
CTFTILT refine option |
False |
Use CTFTILT to refine defocus only in case you tilted the stage. |
Local defocus search range |
3000 |
Using the given search range for CTFTILT to refine locally around CTFFIND maximum (accepted values min=0, max=20000). |
Expected tilt and tilt search range in degrees |
(0, 8) |
Minimum and maximum micrograph tilt to be searched in CTFTILT determination (accepted values min=0, max=80). |
Sample parameter file (expert level)¶
You may run the program in the command line by providing the parameters via a text file:
micctfdetermine --f parameterfile.txt
Where the format of the parameters is:
Micrographs = cs_scan034.tif
Diagnostic plot pattern = micctfdetermine_diag.pdf
Spring database option = False
spring.db file = spring.db
Continue spring.db option = False
Spherical aberration = 2.0
Electron voltage in kV = 200
Amplitude contrast = 0.1
Pixel size in Angstrom = 1.163
Range of defocus in Angstrom = (10000, 45000)
Defocus search step size = 300
Astigmatism search restraint in Angstrom = 2000
Tile size power spectrum in Angstrom = 600
Resolution search range in Angstrom = (30.0, 6.0)
CTFTILT refine option = False
Local defocus search range = 3000
Expected tilt and tilt search range in degrees = (0, 8)
Binning option = True
Binning factor = 2
MPI option = True
Number of CPUs = 2
Temporary directory = /tmp
Command line options¶
When invoking micctfdetermine, you may specify any of these options:
usage: micctfdetermine [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--spring_database_option]
[--continue_spring.db_option] [--ctftilt_refine_option] [--binning_option] [--mpi_option]
[input_output [input_output ...]]
Program to determine CTF parameters from a set of micrographs using CTFFIND and CTFTILT (Mindell and Grigorieff JSB, 2003)
positional arguments:
input_output Input and output files
optional arguments:
-h, --help show this help message and exit
--g, --GUI GUI option: read input parameters from GUI
--p, --promptuser Prompt user option: read input parameters from prompt
--f FILENAME, --parameterfile FILENAME
File option: read input parameters from FILENAME
--c, --cmd Command line parameter option: read only boolean input parameters from command line and all other parameters will be assigned
from other sources
--l LOGFILENAME, --logfile LOGFILENAME
Output logfile name as specified
--d DIRECTORY_NAME, --directory DIRECTORY_NAME
Output directory name as specified
--version show program's version number and exit
--spring_database_option, --spr
If checked will read previous spring.db (Sqlite-compatible database) otherwise will create new one. (default: False)
--continue_spring.db_option, --con
Continue spring.db without re-computing previously determined CTF of micrographs. Do not tick in case you want to update the
Ctf results of the micrographs in the provided database. (default: False)
--ctftilt_refine_option, --ctf
Use CTFTILT to refine defocus only in case you tilted the stage. (default: False)
--binning_option, --bin
Micrograph is reduced in size by binning. (default: False)
--mpi_option, --mpi OpenMPI installed (mpirun). (default: False)
Program flow¶
prepare_micrograph_for_ctffind: Prepare micrographs for CTFFIND.
run_ctffind_for_first_defocus_estimation: Runs CTFFIND on micrographs to determine defocus
run_ctftilt_to_refine_defocus_parameters: Runs CTFTILT on micrographs to refine local defocus
assemble_diagnostic_plot: Assembles summarized diagnostic plot of micrograph.