**PURPOSE**- Creates a 3-D model density distribution. The following options are
available:

1. Blank volume

2. Cylinders

3. Spheres

4. Gaussian spheres/ellpisoids

5. Helix of spheres

6. Test pattern consisting of sine waves

7. Wedge of density Example.

**SEE ALSO****MO**[Create Model image] **BL**[Create Blank image/volume] **MA**[Mask - image/volume with a circular mask] **PT**[Create Pattern or mask image] **LA L**[Put text label inside an image]

**USAGE**- .OPERATION: MO 3

- .OUTPUT FILE: MOD001

[Enter the name for the volume file.].DIMENSIONS (NX, NY, NZ): 100, 100, 100

[Enter volume dimensions.][Following pattern menu appears.]

MENU:

B BLANK, CONSTANT DENSITY C CYLINDERS G GAUSSIAN SPHERE/ELLIPSOID G1 1ST ORDER GAUSSIAN SPHERE/ELLIPSOID (0...1) G2 2ND ORDER GAUSSIAN SPHERE/ELLIPSOID (0...1) G3 3RD ORDER GAUSSIAN SPHERE/ELLIPSOID (0...1) H HELIX OF SPHERES HA HELIX OF SPHERES, ADD DENSITITY NUM LINE NUMBERS R RANDOM DENSITY PATTERN S SINE WAVES T SINE WAVE SP SPHERES SPA SPHERES, ADD DENSITIES SPV SPHERES, VARIABLE DENSITIES W DENSITY WEDGE .OPTION (B/C/H/HA/G/G1/G2/G3/NUM/R/S/SP/SPA/SPV/T/W): SPA

[Enter the desired pattern option.] - For option
**"B" - Blank**. - Creates a blank volume of constant density.
.DENSITY: 7.0

[Enter density value for the volume.] - For Option
**"C" - Cylinder** - Creates cylinder(s) having uniform density.
.BACKGROUND DENSITY: 1

[Enter density for the volume outside of the cylinder(s).].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 in pixels.].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 inside cylinder.].CHOOSE X, Y, Z (or Q TO END CYLINDER ENTRY) Y

[You may specify another cylinder now or enter 'Q' to terminate.] - For Options
**"H/HA" - Helix** - Creates a helical arrangement of spheres running in the Y-direction.
.DENSITY INSIDE SPHERES (or <CR> = 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 NY.] - For Option
**"G" - Gaussian distribution** - Creates a 3D spherical/ellipsoidal Gaussian density distribution normalized such that the
**sum**of all the voxel densities equals 1.0..COORDINATES OF THE CENTER X,Y,Z (or <CR> FOR IMAGE CENTER): 12, 23.12, 33

.RADII IN X,Y,Z ( = STD. DEV.) : 4, 2, 2

[Enter the radii / standard deviations for Gaussian function. Controls radius of mask.] - For Options
**"G1,G2,G3" - Gaussian distribution** - Creates a spherical/elipsoidal Gaussian density distribution normalized such that the
**maximum**voxel density equals 1.0.

'G2' and 'G3' are super-Gaussian masks of order 2 and 3 with squared or cubed Gaussian falloffs and are generally better than 'G1' for most uses. Their densities are described in the form

where n is the order of Super-Gaussian, and a, b, and c are the semi-principal axes of the ellipsoid..CENTER COORDINATES X,Y,Z (or <CR> FOR IMAGE CENTER): 12, 23.12, 33

[Enter center.].RADII IN X,Y,Z ( = STD. DEV.) : 4, 2, 2

[Enter the radii / standard deviations for Gaussian function. Controls radius of mask.] - For Option
**"NUM"- NUMBERS** - Creates a test volume containing numbers. The line number in the 3D file is put into each line at a specified position.
.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.] - For Option
**"R" - Random** - Creates a volume containing random densities.
.GAUSSIAN DISTRIBUTED? (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.] - For Option
**"S" - Sine.** - Creates a volume containing a 3-D distribution from an arbitrary number of 3-D sine waves with arbitrary spatial frequency vectors.
.NUMBER OF SINE WAVES: 3

[Enter number of sine waves, with a maximum of 50.].I=1 AMPLITUDE, SPATIAL FREQ. IN (X,Y,Z): 0.5, 1,2,4

.I=2 AMPLITUDE, SPATIAL FREQ. IN (X,Y,Z): 1.0, 2,2,2

.I=3 AMPLITUDE, SPATIAL FREQ. IN (X,Y,Z): 1.0., 1,2,1

[Enter relative amplitude and spatial frequency for each sine wave.][The actual amplitudes used (AMPL) are calculated from the input amplitudes (AMPLIN) 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.] - For Options
**"SP/SPA/SPV"** - Creates a volume with spheres of given outer and inner radius and a given density, with centers located at specified points. The default inner radius is zero and the default density value is 2.0. After modelling a sphere of a given radius the program should ask for the radii (but does not) and location of the next sphere. If the any spheres outer radius exceeds the boundary of the 3-D file, the program warns that part of the sphere will be truncated.
.GET COORDINATES FROM DOCUMENT FILE (Y/N): N

[Otherwise the user will input sphere coordinates from the command line.] - If the answer is 'Y' SPIDER asks:

.DOCUMENT FILE: DOC001

[Enter name of document file containing center coordinates of spheres, in order: X,Y,Z ( ,Radius2, Radius1 - optional) (,Mass value - optional) starting in any column].NUMBER OF SPHERES, STARTING COL. FOR X,Y,Z: 50, 1

[Enter number of spheres and column of X-coordinates in the document file].X, Y, & Z OFFSET: 20.0, -10.0, 510.

[Enter offset for X,Y,Z]- For Option
**"SP/SPA"**:

.DENSITY INSIDE SPHERES (or <CR> = 2.0): 1.0

[Enter the density value to placed inside sphere.]- For Options
**"SP/SPA/SPV"**with input from a doc file:

.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. But, the outer radius can be taken from the document file while the inner one can be fixed for all spheres and entered explicitly.]- For Options
**"SP/SPA/SPV"**without input from a doc file:

.OUTER AND INNER RADII OF SPHERES: 4.5, 1.7

[Enter radius of sphere as a floating point number.].CENTER COORDINATES X,Y (or <CR> FOR IMAGE CENTER): 10, 10, 15

[Enter the coordinates for center the sphere. To exit: enter '0, 0, 0' as coordinates.]- For Option
**"T" - Test** - Creates a three-dimensional (circularly continuous) sine wave with spatial frequency: (1,1,1).
- For Option
**"W" - Wedge** - Creates a three-dimensional, linearly increasing density distribution. The voxel values increase linearly with increasing X, Y, and Z.

**SUBROUTINES**- MODEL3, RANN

**CALLER**- UTIL1

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