| -action correct | Action: 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). | |
| -invertaxis | Inverts the tilt axis to correct for improper setup. |
| -filter | Filter extremes before doing anything with the image. |
| -background | Correct background after applying CTF (default not). |
| -fitastigmatism 2 | Fit astigmatism for individual micrographs (1) or combined (2) (default not). |
| -toparticle | Transfer micrograph CTF parameters to particle records (default not). |
| -ctf 512,512,2 | Generate a CTF image of this size with flag: 1=center, 2=power, 3=both. |
| -simulate | Simulate a tilted CTF for each x or y-line. |
| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -mgpath dir/subdir | Set the micrograph file paths. |
| -pspath dir/subdir | Set the power spectrum file paths. |
| -partpath dir/subdir | Set the particle file paths. |
| -tile 1024,1024,1 | Size of power spectrum generated during preparation (default 512,512,1). |
| -micrograph | Use micrograph file given in parameter file instead of particle file. |
| -frames | Use micrograph frames file given in parameter file instead of particle file. |
| -sampling 1.5,1.5,1.5 | Sampling (angstrom/pixel, a single value sets all three). |
| -resolution 27.5,125.3 | Resolution limits for CTF determination and application (default 0.1,1e6). |
| -wiener 0.15 | Wiener factor for CTF correction (default 0.2). |
| Microscope parameters: | |
| -Volt 100 | Set the acceleration voltage (default 120 kV). |
| -Amplitude 0.07 | Set the amplitude contrast (default 0.07). |
| -Cs 2.0 | Set the spherical aberration, Cs (default 2.0 mm). |
| -Cc 2.0 | Set the chromatic aberration, Cc (default 2.0 mm). |
| -alpha 0.15 | Set the illumination half-angle (default 0.1 milliradians). |
| -energyspread 0.9 | Set the effective energy spread (default 1 eV). |
| -aperture 100 | Aperture size (default 100 µm). |
| -focallength 2.5 | Focal length (default 3.5 mm). |
| -slitwidth 25 | Energy filter slit width (default 0 eV - no filter). |
| Imaging parameters: | |
| -Defocus 1.2,1.0,47 | Defocus average & deviation, and astigmatism angle (default 2 um, 0 um, 0). |
| -Astigmatism 0.3,-34 | Set defocus deviation and astigmatism angle (um, degrees). |
| -axis 74.7 | Tilt axis angle relative to x-axis (default 0 or from parameter file). |
| -tilt 15 | Tilt angle (default from parameter file). |
| -basetype 2 | Baseline 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). | |
| -baseline | 1,1.5,-2.6,12.9,30,118 Baseline type and 4 or 5 coefficients: (default 1,0,0,0,0) |
| -envtype 3 | Envelope 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). | |
| -envelope | 28,-563,0.78,-215 Envelope coefficients: Double gaussian with 4 coefficients (default 1,-10,0,0). |
| Fitting parameters: | |
| -Range 0.6,3.5,0.2 | Defocus minimum, maximum and increment for fitting (default 0.1,20,0.1 um). |
| -json file.json | Input JSON file with CTF parameters. |
| -output file.star | Output parameter file. |
| -jsonout file.json | Output CTF parameters to a JSON file. |
| -PSaverage file.mrc | Output average power spectrum. |
| -Postscript file.ps | Postscript output file name for CTF fit. |
| -Histogram file.ps | Postscript output file name for defocus histogram. |
| -Plotastigmatism file.ps | Postscript output file name for astigmatism. |
| -Average file.ps | Postscript output file name for average of all CTF curves. |
| -Zeroes file.ps | Postscript output file name for defocus-vs-zeroes plot. |
| -Envelope file.ps | Envelope curve output file name. |
| -Pointspread file.ps | Point spread curve output file name. |
| -Function ctf.mrc | Contrast transfer function output file name. |
| 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) | |