Bsoft program

bctf

Usage: bctf [options] input.star/input.img [input2.star/output.img]

Applies, determines or corrects for the CTF (contrast transfer function) in electron micrographs.

Actions:

-action correctAction: 1=flip, 2=apply, 3=correct, 4=wienerfilter,
5=baseline, 6=baseline2, 7=baseflip, 8=basecorrect,
11=prepare, 12=fit, 13=prepfit (default 0=none).
-invertaxisInverts the tilt axis to correct for improper setup.
-filterFilter extremes before doing anything with the image.
-backgroundCorrect background after applying CTF (default not).
-fitastigmatism 2Fit astigmatism for individual micrographs (1) or combined (2) (default not).
-toparticleTransfer micrograph CTF parameters to particle records (default not).
-ctf 512,512,2Generate a CTF image of this size with flag: 1=center, 2=power, 3=both.
-simulateSimulate a tilted CTF for each x or y-line.

Parameters:

-verbose 7Verbosity of output.
-datatype uForce writing of a new data type.
-mgpath dir/subdirSet the micrograph file paths.
-pspath dir/subdirSet the power spectrum file paths.
-partpath dir/subdirSet the particle file paths.
-tile 1024,1024,1Size of power spectrum generated during preparation (default 512,512,1).
-micrographUse micrograph file given in parameter file instead of particle file.
-framesUse micrograph frames file given in parameter file instead of particle file.
-sampling 1.5,1.5,1.5Sampling (angstrom/pixel, a single value sets all three).
-resolution 27.5,125.3Resolution limits for CTF determination and application (default 0.1,1e6).
-wiener 0.15Wiener factor for CTF correction (default 0.2).
Microscope parameters:
-Volt 100Set the acceleration voltage (default 120 kV).
-Amplitude 0.07Set the amplitude contrast (default 0.07).
-Cs 2.0Set the spherical aberration, Cs (default 2.0 mm).
-Cc 2.0Set the chromatic aberration, Cc (default 2.0 mm).
-alpha 0.15Set the illumination half-angle (default 0.1 milliradians).
-energyspread 0.9Set the effective energy spread (default 1 eV).
-aperture 100Aperture size (default 100 µm).
-focallength 2.5Focal length (default 3.5 mm).
-slitwidth 25Energy filter slit width (default 0 eV - no filter).
Imaging parameters:
-Defocus 1.2,1.0,47Defocus average & deviation, and astigmatism angle (default 2 um, 0 um, 0).
-Astigmatism 0.3,-34Set defocus deviation and astigmatism angle (um, degrees).
-axis 74.7Tilt axis angle relative to x-axis (default 0 or from parameter file).
-tilt 15Tilt angle (default from parameter file).
-basetype 2Baseline type: (default 1)
Type 1: Polynomial with 5 coefficients.
Type 2: Double Gaussian with 5 coefficients.
Type 3: EMAN style with 4 coefficients.
Types 4-6: 1-3 with gaussian fit of water ring (only for high resolution limit < 3 A).
-baseline1,1.5,-2.6,12.9,30,118 Baseline type and 4 or 5 coefficients: (default 1,0,0,0,0)
-envtype 3Envelope type: (default 4)
Type 1: Single gaussian (2 coefficients).
Type 2: Single gaussian with constant (3 coefficients).
Type 3: Double gaussian (4 coefficients).
Type 4: Double gaussian with constant (5 coefficients).
-envelope28,-563,0.78,-215 Envelope coefficients: Double gaussian with 4 coefficients (default 1,-10,0,0).
Fitting parameters:
-Range 0.6,3.5,0.2Defocus minimum, maximum and increment for fitting (default 0.1,20,0.1 um).

Input:

-json file.jsonInput JSON file with CTF parameters.

Output:

-output file.starOutput parameter file.
-jsonout file.jsonOutput CTF parameters to a JSON file.
-PSaverage file.mrcOutput average power spectrum.
-Postscript file.psPostscript output file name for CTF fit.
-Histogram file.psPostscript output file name for defocus histogram.
-Plotastigmatism file.psPostscript output file name for astigmatism.
-Average file.psPostscript output file name for average of all CTF curves.
-Zeroes file.psPostscript output file name for defocus-vs-zeroes plot.
-Envelope file.psEnvelope curve output file name.
-Pointspread file.psPoint spread curve output file name.
-Function ctf.mrcContrast transfer function output file name.

Examples:

To apply the CTF:
bctf -verbose 7 -action apply -Defocus 2.3 input.img distorted.img
To prepare a power spectrum from a micrograph and to fit the CTF:
bctf -v 7 -datatype float -action prepfit -sam 1.842 -out new.star mg0001.tif mg0001_ps.pif
This is a good way to generate the initial STAR file for each micrograph
of a single particle analysis effort, as well as a power spectrum file.
Subsequently, the automatic fit should be checked and corrected in bshow.
To correct for the CTF by simply flipping the phases in every second Thon ring:
bctf -verbose 7 -action flip -Defocus 1.4 part.pif part_flip.pif
Applying the same flipping operation twice will recover the original image.
To correct for the CTF:
bctf -v 7 -action correct -Defocus 1.9 -wiener 0.1 part.pif part_corr.pif
The equation used for the correction is:
U = I*C/(C^2 + w)
where:
U: corrected image
I: distorted image
C: CTF
w: Wiener factor, default 0.2
To correct for the CTF with baseline compensation:
bctf -v 7 -act baseline -Def 1.2 -wien 0.2 -base 1,1.5,-2.6,12.9,30,118 part.pif part_corr.pif
The equation used for the correction is:
U = I*C/(B*C^2 + w)
where:
U: corrected image
I: distorted image
C: CTF
B: baseline
w: Wiener factor, default 0.2
Baseline equations:
1. a0 + a1*s + a2*s^2 + a3*s^3 + a4*s^4
2. a0 + a1*e^(a2*s^2) + a3*e^(a4*s^2)
3. a0 + a1*e^(a2*s^0.5 + a3*s^2)

Bsoft version 2.0.7-20200917 (64 bit)


Generated by bdoc.pl on Mon Oct 26 08:20:11 2020


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