.DEBUG OUTPUT: 0
[Answer: 0 otherwise very large amounts of output are produced]
.TEMPLATE FOR 2D RADON OUTPUT: *
[If * is answered no output is produced. Otherwise every
Radon transform (i.e. one for every combination of theta and
phi) that is extracted from the 3D Radon transform is written
to disk.]
.TEMPLATE FOR CCF OUTPUT: *
[If * is answered no ouptu is produced. Otherwise for each
combination of theta and phi one cross-correlation function
between the input and the extracted Radon transform is written
to disk.]
.3D RADON FILE: 3DRAD001
[Enter the name of the 3D Radon transform.]
.2D RADON FILE: RAD2D001
[Enter name of two-dimensional Radon transform.]
.SAMPLING RANGE AND INCREMENT IN EXTRACTED RADON TRANSFORM:
.ALPHA FROM,TO (DEF=2D): -90,88
.INCREMENT (DEF=2D: 2
[Enter parameter for the Radon transforms that are extracted
from the 3D transform. The default is the same sampling as
the 2D Radon transform.]
.PEAK FILE: peak001
[Enter name of file for the 3D angular cross-coraltion function.]
.(S)HIFTALIGN,(N)O SHIFTALIGN: S
[Enter S if a simultaneous translational alignment is desired.]
.(S)UBSEARCH OR (C)OMPLETE SEARCH?(=DEF): C
[Answer C. S has not been developed sufficiently.]
.THETA RANGE OF SEARCH (FROM,TO): -90,80
.INCREMENT: 10
[Enter search range and incement for theta (second Euler angle
around y-axis.]
.PHI RANGE OF SEARCH (FROM,TO): -180,170
.INCRMENT: 10
[Enter search range and increment of first Euler Angle. (around
z-axis.]
.PSI RANGE OF SEARCH (FROM,TO): -180,170
.INCREMENT: 10
[Enter search range of third Euler angle (around z'-axis, within
the 2D projection plane.]
Remark: For refinement these angular ranges and increments should be chosen around the crude alignment values.
.(P)ASE CORRELATION: P
[Answer P if the cross-correlation is done with the Fourier
coefficients normalized by their value. A Wiener style filter
is applied. If NF is the new Fourier coefficient and OF is the
old value the normalization formula is:
NF = OF / (|OF| + epsilon).
.FOURIER FILTER Y/N: Y
[Enter Y if you want to Fourier filter during the correlation.]
.# OF FILTRATIONS 1/2: 2
[Enter 2 if you want to combine two filters, 1 if only
one filter is to be used.]
.(A)DDITIVE (=DEF),(M)ULTIPLICATIVE: M
[Combine the chosen filters either additive or multiplicative.
For a band pass filter M is the ususal option.]
.(1)L.P./(2)H.P./(3)G.L.P./(4)G.H.P./(5)F.L.P./(6)F.H.P.,(7) R*: 5
[Enter desired filter. Similar to SPIDER opreation FF.
1: cutoff low pass filter, 2: cutoff high pass filter
3: Gaussian low pass filter, 4: Gaussian high pass filter.
5: Fermi low-pass filter, 6: Fermi high pass filter.
7: Multiplication with r* (the Fourier radius).
.FILTER RADIUS: 0.123
[Enter filter radius. also otion 7 currently asks for a radius,
but the value is ignored.]
NOTES