Function of the program:   Forward and Backward FFT of 3-D map. The program can read the map directly from PIF format and calculate the FFT. The calculated structure factors can be used by the program EMRESOL (below) to calculate the resolution, or can be used by the program EMFOM to do filtering, or can be used by many X-ray crystallography software packages, such as CNS/X-Plor. Structure factors calculated from CNS/X-Plor can be read by MAPFFT to calculate backward FFT to obtain a PIF map. The obtained PIF map can be used for difference map calculation or can be used as the initial model for cryo-EM reconstruction.

Function of the program:   Forward and Backward FFT of 2-D boxed images. The program can read directly of PIF image and then calculate the structure factors. The structure factor calculated from all the boxed images of the same micrograph can be averaged and then a further circular averaging of the 2-D averaged FFT can be done. The circular averaged data can be used for estimate the defocus value by the program CTFEST (below). After obtaining the defocus value of the micrograph, back transfer with different type of CTF corrections can be done by IMGFFT. Temperature factor correction can also be done when doing the back transfer.

Purpose of the program:   The old FFT library used in EM reconstruction is from 70s as mentioned above. Padding (adding zeros) is required for the image FFT to meet the dimension requirement of the old FFT library. Not only time is wasted for the padding operation, but also some artifacts have been added to the back transferred images. The new FFTW library has no dimension limitations. Padding is skipped. The FFT is faster and more flexible. CTF correction and temperature factor correction can be tested at the level of raw images before doing cryo-EM reconstruction.

Usage of the program:

• Usage: imgfft [option] image.pif image.asf

• Options:

  Options	explanations
  -F	Forward FFT (default)
  -B	Backward correct FFT, without CTFEST file
  -r hi_resolution	Highest Resolution in E
  -l low_resolution	Lowest resolution in E
  -p pixel_size	Pixel_size in E, default is from the PIF header
  -s amp_scale_factor	Amp scale factor, Default 1.0
  -k img_scale_factor	Image density scale factor, output default 1.0
  -t	Input and Output SF are strict format TSB ASCII SF
  -x	Input and Output SF are X-Plor SF
  -f	Soft filter using the default parameters
  -e recipocal_step edge_cut_weight	Soft filter parameters,after reciprocal_step grids in reciprocal space,the weight drops to edge_cut_weight Default recipocal_step=3.0;edge_cut_weight=0.000001
  -m Manipulate_Flag	1 = rotate 90 degree; 2 = translate 1/2,1/2,1/2;3 = both
  -L	The output will be in log scale
  -w	Output the whole set of the SF, default is half set
  -V	Write out the Vector Averaged FFT at the end
  -A	Write out the Amplitude Averaged FFT at the end
  -i	Write out the Intensity Averaged FFT at the end
  -I	Only write out the Intensity Averaged FFT
  -c	Write out the circular averaged at the end
  -C	Only write out the circular averaged results
  -B CTFEST_OUTPUT_FILE	Backwork FFT with B_factor and CTF correction read in Famp,Cs,Voltage,Defocus, B_factor from CTFEST file
  -b B_factor	read in B_factor, doing B_factor correction
  -D CTFEST_OUTPUT_FILE	Backwork FFT with only CTF phase correction read in Famp,Cs,Voltage,Defocus from CTFEST file
  -d defocus_value_in_nm	read in defocus value and backwork FFT with CTF phase correction
  -X Famp	change the Famp, default is 0.05.
  -Y Cs	change the Cs, default is 2.0 mm
  -Z Voltage	change the voltage, default is 300 kV.
  -W weiner factor	Add additional ctf/(ctf2+weiner) amplitude correction
  -h	Print the help, no calculation

• Example for IMGFFT:

  Image -> Circular Averaged SF:	imgfft -p 3.11111 -C image.pif image.sf
  Image -> CTF and B factor Corrected Image:	imgfft -p 3.11111 -D image.ctfest -b 28.0 -W 0.5 image.pif image_prefix