radialft_asym implements the last step of constructing a CTF for use
in deconvolution. It radially averages a 3D Fourier
transform of a measured point source (the transform could be performed with
Priism's FTransform3D) and writes the result in
the format expected by the deconvolution application.
To use radialft_asym, invoke it from the command line. The expected form
of the command line is (optional parts are shown in brackets):
radialft_asym transform_file ctf_file -cofm=x:y:z \
[-flip] [-makereal] [-fixaxes=flag]
The meanings of the different entries on the command line are:
- transform_file
- transform_file is expected to be the name of a Priism image
file which holds the result of a real->complex 3D Fourier transform
where the redundant negative x frequencies are not retained (i.e.
for Priism's FTransform3D do not use
the 'fully complex' option) and the zero frequency component is at the
lower left corner of the first section (i.e. for Priism's FTransform3D do
no use the "zero frequency centered" option). radialft_asym accepts two
possible orderings of the dimensions in transform_file. The
default is to expect that the transform rearranged the dimensions so that
the untransformed arrangement (x,y,z) became (z,x,y). This is the format
generated by the old command-line program, threedfftpjs. If the -flip
option is supplied, radialft_asym assumes that transform_file
is in the other accepted format where the transform did not rearrange the
dimensions (Priism's FTransform3D
generates this alternative format). radialft_asym expects that the pixel
spacings in the header of transform_file are the unrearranged
pixel spacings of the transformed data and that the spacings have not been
converted to frequency units. Because of a limitation in the
deconvolution program, the x, y, and z dimensions of
transform_file should be no bigger than 512 x 257 x 512 (or
257 x 512 x 512 if -flip is used).
- ctf_file
- ctf_file is the name of the CTF file to generate.
-cofm=x:y:z
- The -cofm (center-of-mass) option is required in order to correct for
the point source's displacement from the origin. If the phases have
already been corrected for the shift, use
-cofm=0:0:0.
Assuming the Fourier transform was done with threedfftpjs or with
FTransform3D, x, y, and z are the
estimated pixel coordinates for the point source in the untransformed data.
If you use another Fourier transform implementation, the signs on
x, y, and z may need to be changed to be
consistent with the sign(s) used in the Fourier transform. With the
-flip option, radialft_asym assumes the Fourier transform
used a negative sign in the complex exponential. Without the
-flip option, radialft_asym assumes that the net effect of
the transform (which in the case of threedfftpjs is done first in xy and
then in z) is to have used a negative sign for the x and y dimensions but
not for the z dimension.
-flip
- If -flip is supplied, radialft_asym assumes that the 3D Fourier
transform did not rearrange the dimensions. Use this option when running
radialft_asym on the output of
Priism's FTransform3D.
-makereal
- If -makereal is specified, the output CTF is the amplitude of the
radially averaged input data and is therefore real-valued. If the CTF
is to be used for 2D deconvolutions, it must be real-valued.
-fixaxes=flag
- The zero frequency components (the components along the x and y axis)
of the CTF are frequently contaminated by artifacts unrelated to the point
source. One source of error is calibration inaccuracies in the gain and
offset for individual CCD pixels; this contributes to terms along the y
(i.e. radial) axis of the CTF. One way to attempt to correct for these
artifacts is to use the -fixaxes option which will cause the components
along the y axis (if flag is greater than or equal to one)
or both the x and y axes (if flag is greater then equal to two)
to be replaced with values determined from the nearest off-axis components.
Related Priism Topics
Deconvolution |
3D Fourier transform |
Priism