.ENTER DIMENSIONS (NSAM,NROW): 32,32
[Enter number of samples and rows.]
.ENTER NUMBER OF SLICES (NSLICE): 16
[Following menu appears.]
.MENU:
(B)LANK -- CONSTANT DENSITY
(C)YLINDER -- SET OF CYLINDERS
(H)ELIX -- HELIX OF SPHERES
(HA) -- HELIX OF SPHERES, ADD DENSITITY
(NUM)BERS -- LINE NUMBERS
(Q)UICK -- RANDOM UNIFORM/GAUSSIAN STATISTICS
(R)ANDOM -- RANDOM UNIFORM/GAUSSIAN STATISTICS
(S)INE -- SET OF SINE WAVES
(SP)HERE -- SET OF SPHERES
(SPA) -- SET OF SPHERES, ADD DENSITIES
(SPV) -- SET OF SPHERES, VARIABLE DENSITIES
(T)EST -- 3D SINE WAVE
(W)EDGE -- DENSITY WEDGE
.B/C/H/HA/NUM/Q/R/S/SP/SPA/SPV/T/W: SPA
[Enter the desired menu option.]
.CONSTANT BACKGROUND: 7.0
[Enter intensity value for the image.]
.VALUE OF VOLUME BACKGROUND: 0
[Enter value the volume outside of the cylinder(s) will
be filled with]
.CHOOSE X, Y, Z (OR Q TO END CYLINDER ENTRY): Y
[Give axis direction of cylinder]
.RADIUS, HEIGHT: 4.5,6.2
[Give radius and height of cylinder.]
.X & Y COORDINATES OF CENTER: 12.,4.3
[Enter X, Y coordinates of center.]
.Z COORDINATE, DENSITY: 7.8,2
[Enter Z coordinate of center, and density value.]
.CHOOSE X, Y, Z (OR Q TO END CYLINDER ENTRY) Y
[You may specify another cylinder now or enter 'Q' to
terminate.]
.ENTER MASS VALUE PER VOXEL (DEFAULT = 2.0):
.SPHERE RADIUS, HELIX RADIUS: 4.2, 8.5
[Enter the radiI for spheres and helix.]
.NO. OF SPHERES, NO. OF TURNS: 12,2
[Enter the total number of sphereS and the total number
of turns in NROW.]
.POSITION IN LINE: 5
[Enter the position where the line number should be
put in each line]
.SCALING FACTOR: 3
[Enter scaling factor]
.NUMBER PIXELS IN LINE? (Y/N): Y
[If answer is "Y" following two questions appear.]
.SLICE NUMBER, LINE NUMBER: 3,4
[Enter slice number and line number]
.SCALING FACTOR: 2
[Enter scaling number]
.GAUSSIAN DISTRIBUTION? (Y/N): N
[For 'N' a random image with the values uniformly distributed
between 0 and 1 is generated. If 'Y' was specified,
SPIDER will ask]
.MEAN AND STANDARD. DEVIATION. OF GAUSSIAN DIST.: 0.0,0.35
[Enter the mean value and standard deviation of the gaussian
distribution for random numbers to be generated.]
SCALING NEW_VALUE = OLD_VALUE * F + C')
.ENTER C, F (DEFAULTS = 0,1)': 0.0, 1.0
[This random generator is the faster one of the two, yet in power of 2 images random generator creates image with a noisy, sine-shaped periodicity in the power spectrum. If the frequency distribution of the noise is critical option 'R' should be used.]
.GAUSSIAN DISTRIBUTION? (Y/N): N
[For 'N' a random image with the values uniformly distributed
between 0 and 1 is generated. If 'Y' was specified,
distributed noise is created, SPIDER will ask:]
.MEAN AND STANDARD. DEVIATION. OF GAUSSIAN DIST.: 0.0,0.35
[Enter the mean value and standard deviation of the gaussian
distribution for random numbers to be generated.]
.NUMBER OF SINE WAVES: 3
[Enter number of sine waves, with a maximum of 20.]
.I=1 REL.AMPL.,SPATIAL FREQUENCY(KX,KY,KZ): .5,1,2,4
.I=2 REL.AMPL.,SPATIAL FREQUENCY(KX,KY,KZ): 1.,2,2,2
.I=3 REL.AMPL.,SPATIAL FREQUENCY(KX,KY,KZ): 1.,1,2,1
[Enter relative amplitude and spatial frequency for
each sine wave.]
[The actual amplitudes used "AMPL" are calculated from
the input amplitudes according to the formula:
AMPL = 2. * AMPLIN / AMPSUM
where "AMPSUM" is the sum of all input amplitudes. A
list of the actual amplitudes is printed out.]
.GET COORDINATES FROM DOCUMENT FILE (Y/N): N
[Otherwise the user will input sphere coordinates from the
command line.]
.NUMBER OF SPHERES, STARTING COL. FOR X,Y,Z: 50,1
[Enter number of spheres and column of X-coordinate
in document file]
.X,Y, & Z OFFSET: 20.,-10.,51.
[Enter offset for X,Y,Z]
.OUTER AND INNER RADII OF SPHERES: 4.5,1.7
[Enter radius of sphere as a floating point number.
If a negative value is entered for one or both of the
radii, they are taken from the document file. If
the inner radius is taken from the document file, the
outer radius also must be in this file, the outer
radius can be taken from the document file while the inner
one can be fixed for all spheres and enetered explicitly.]