mrcImageModelCreate
mrcImageModelCreate is Eos's Command that creates the model image.
Contents
- 1 List of option
- 2 Execution example
- 2.1 Example of options only essential
- 2.2 Option -nx, -ny, -nz
- 2.3 Option -r
- 2.4 Option -lx, -ly, -lz
- 2.5 Option -m
- 2.5.1 Case: m=1, nx=69, ny=69
- 2.5.1.1 Case: No other settings
- 2.5.1.2 Case: -i Specify Input file
- 2.5.1.3 Case: lx=2.5, ly=7.5, lz=10.0
- 2.5.1.4 Case: radius=100
- 2.5.1.5 Case: n=5
- 2.5.1.6 Case: dz=71
- 2.5.1.7 Case: n=20, dz=7
- 2.5.1.8 Case: dphi=20, n=20, dz=7
- 2.5.1.9 Case: phi=5, n=20, dz=7
- 2.5.1.10 Case: sz=100, ez=300, n=20, dz=7
- 2.5.2 Case: m=2
- 2.5.3 Case: m=3
- 2.5.4 Case: m=4
- 2.5.5 Case: m=5
- 2.5.6 Case: m=6
- 2.5.7 Case: m=7
- 2.5.1 Case: m=1, nx=69, ny=69
List of option
Main option
| Option | Essential/Optional | Description | Default |
|---|---|---|---|
| -o | Essential | Output: mrcImage | NULL |
| -i | Optional | Input | NULL |
| -nx | Optional | Real length = nx * lx | 70 |
| -ny | Optional | Real length = ny * ly | 70 |
| -nz | Optional | Real length = nz * lz | 100 |
| -r | Optional | radius[pixel] | 1 |
| -lx | Optional | Pixel Size[Angstrom] | 5.0 |
| -ly | Optional | Pixel Size[Angstrom] | 5.0 |
| -lz | Optional | Pixel Size[Angstrom] | 5.0 |
| -radius | Optional | filament radius [A] | 150 |
| -n | Optional | n-helix | 3 |
| -dz | Optional | pitch [A] | 143 |
| -dphi | Optional | rotation angle [degree] | 40 |
| -phi | Optional | rotation angle in the same level [degree] | 120 |
| -sz | Optional | start z [A] | 0 |
| -ez | Optional | end z [A] | 500 |
| -sphi | Optional | start angle [degree] | 0 |
| -sphi2 | Optional | start angle 2 [degree] | 40 |
| -inMode | Optional | inMode | 0 |
| -units | Optional | units number | 9 |
| -fm | Optional | formation | 0 |
| -c | Optional | ConfigurationFile | NULL |
| -m | Optional | Mode | 0 |
| -h | Optional | Help |
-m details
| Value | Description |
|---|---|
| 0 | Circle(a right cylinder:3D) and Triangle(a trigonal prism:3D) Optional argument : -nx -ny -nz -r |
| 1 | Thick Filaments
Example
Optional argument
-nx -ny -nz Image Size
-lx -ly -lz Pixel Size
-radius filament radius 150[A]
-n three helix
-dz pitch 143[A]
-dphi rotation angle 40[degree]
-phi rotation angle in the same level 120[degree]
-sz start z 0[A]
-ez end z 800[A]
-sphi start phi 0[degree]
-----------------------
-inMode Centre = 0
-inMode Origin = 1
-----------------------
-units 9
-fm formation of Gauss Sphere (t=1, u=9 and n=3)
0: normal
1: 3 sphere on the same z
Phi 0 , 30 , 60 degree
2: 3 sphere on the differnt z and on the differnt radius
Phi 0 , 30 , 60 degree
Z 0 , 30 , 60 A
Radius 0 ,1.2 ,1.4 times
3: 3 sphere on the same z and on the different radius
Phi 0 , 30 , 60 degree
Z 0 , 0 , 0 A
Radius 0 ,1.2 ,1.4 times
-----------------------
-units 3
-fm formation of Gauss Sphere (t=1, u=3 and n=3)
0: abnormal
|
| 2 | Dot(2D) |
| 3 | Projection of 2 Sphere and 2 circle for 2D Optional argument : -nx -ny |
| 4 | Another Projection of 2 Sphere and 2 circle for 2D Optional argument : -nx -ny |
| 5 | Another Projection of 2 Sphere for 2D Optional argument : -nx -ny |
| 6 | SheppLogan 2D Optional argument : -nx -ny |
| 7 | SheppLogan 3D Optional argument : -nx -ny -nz |
Execution example
Example of options only essential
 |
Min Max |
0 (0, 0, 0) 2 (34, 35, 50) |
N : ( 70, 70, 100) Mode : 2 mrcFloatImage StartN : ( 0, 0, 0) M : ( 1, 1, 1) Length : ( 5.000, 5.000, 5.000) A,B,G : ( 90.00, 90.00, 90.00) C,R,S : ( 1, 2, 3) Min,Max,Mean : ( 0, 2, 0.493)
Option -nx, -ny, -nz
Case: nx=50, ny=100, nz=150
 |
Min Max |
0 (0, 0, 0) 2 (25, 50, 74) |
N : ( 50, 100, 150) Mode : 2 mrcFloatImage StartN : ( 0, 0, 0) M : ( 1, 1, 1) Length : ( 5.000, 5.000, 5.000) A,B,G : ( 90.00, 90.00, 90.00) C,R,S : ( 1, 2, 3) Min,Max,Mean : ( 0, 2, 0.745)
Option -r
Case: r=100
 |
Min Max |
1 (0, 0, 0) 2 (0, 1, 0) |
N : ( 70, 70, 100) Mode : 2 mrcFloatImage StartN : ( 0, 0, 0) M : ( 1, 1, 1) Length : ( 5.000, 5.000, 5.000) A,B,G : ( 90.00, 90.00, 90.00) C,R,S : ( 1, 2, 3) Min,Max,Mean : ( 1, 2, 1.49)
Option -lx, -ly, -lz
Case: lx=2.5, ly=7.5, lz=10.0
 |
Min Max |
0 (0, 0, 0) 2 (34, 35, 50) |
N : ( 70, 70, 100) Mode : 2 mrcFloatImage StartN : ( 0, 0, 0) M : ( 1, 1, 1) Length : ( 2.500, 7.500, 10.000) A,B,G : ( 90.00, 90.00, 90.00) C,R,S : ( 1, 2, 3) Min,Max,Mean : ( 0, 2, 0.493)
Option -m
Case: m=1, nx=69, ny=69
Case: No other settings
|
|
Min Max |
0 (0, 0, 0) 1 (19, 8, 0) |
Case: -i Specify Input file
-i Input file's image
|
|
Min Max |
7.97113e-11 (0, 0, 0) 8.32888 (3, 15, 8) |
Output file
|
|
Min Max |
0 (0, 0, 0) 8.32888 (64, 34, 0) |
Note that Input file's Length doesn't reflect to Output file.
Case: lx=2.5, ly=7.5, lz=10.0
|
|
Min Max |
0 (0, 0, 0) 1 (4, 17, 0) |
Case: radius=100
|
|
Min Max |
0 (0, 0, 0) 1 (24, 17, 0) |
Case: n=5
|
|
Min Max |
0 (0, 0, 0) 1 (43, 5, 0) |
Case: dz=71
|
|
Min Max |
0 (0, 0, 0) 1 (19, 8, 0) |
Case: n=20, dz=7
|
|
Min Max |
0 (0, 0, 0) 1 (34, 4, 0) |
Case: dphi=20, n=20, dz=7
|
|
Min Max |
0 (0, 0, 0) 1.13578 (58, 16, 99) |
Case: phi=5, n=20, dz=7
|
|
Min Max |
0 (0, 0, 0) 1.39997 (64, 34, 99) |
Case: sz=100, ez=300, n=20, dz=7
|
|
Min Max |
0 (0, 0, 0) 1 (34, 4, 20) |
Case: m=2
 |
Min Max |
0 (0, 0, 0) 1 (17, 17, 0) |
Case: m=3
 |
Min Max |
0 (0, 0, 0) 40 (42, 40, 0) |
Case: m=4
 |
Min Max |
0 (0, 0, 0) 24 (33, 29, 0) |
Case: m=5
 |
Min Max |
0 (0, 0, 0) 13 (34, 34, 0) |
Case: m=6
 |
Min Max |
0 (0, 0, 0) 2 (33, 3, 0) |
Case: m=7
 |
Min Max |
0 (0, 0, 0) 2 (35, 35, 5) |
