Difference between revisions of "mrcImageModelCreate"

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(Created page with "'''mrcImageModelCreate''' is Eos's Command that creates the model image. == List of option == === Main option === <table border="1"> <tr> <th>Option</th>...")
 
(→‎Case: m=1, nx=69, ny=69)
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</tr>  
 
</tr>  
 
</table>  
 
</table>  
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<br>
 +
 +
=====Case: -i Specify Input file=====
 +
[[Media:Input-GaussSphere.mrc|-i Input file]]'s image
 +
<table>
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<tr>
 +
<td><p align="Center">[[File:Input-GaussSphere.png]]<br>
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xy-plane<br></p>
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</td>
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<td><p align="Center">[[File:Input1-GaussSphere.png]]<br>
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yz-plane<br></p>
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</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
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</td>
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<td><p align="left">7.97113e-11 (0, 0, 0)<br>
 +
8.32888 (3, 15, 8)<br>
 +
0.223545<br>
 +
0.859713<br>
 +
0.0130319<br></p>
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</td>
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</tr>
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</table>
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 +
Output file<br>
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<table>
 +
<tr>
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<td><p align="Center">[[File:Outdata-m1i-mrcImageModelCreate.png]]<br>
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xy-plane<br></p>
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</td>
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<td><p align="Center">[[File:Outdata1-m1i-mrcImageModelCreate.png]]<br>
 +
yz-plane<br></p>
 +
</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">0 (0, 0, 0)<br>
 +
8.32888 (64, 34, 0)<br>
 +
0.0220142<br>
 +
0.264693<br>
 +
0.000383612<br></p>
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</td>
 +
</tr>
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</table>
 +
<br>
  
 
=====Case: lx=2.5, ly=7.5, lz=10.0=====  
 
=====Case: lx=2.5, ly=7.5, lz=10.0=====  
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</table>
  
 
====Case: m=2====  
 
====Case: m=2====  

Revision as of 00:45, 10 September 2014

mrcImageModelCreate is Eos's Command that creates the model image.


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

Outdata-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

2 (34, 35, 50)
0.492871
0.499957

0.000714225

 
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

Outdata-nx50ny100nz150-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

2 (25, 50, 74)
0.745009
0.435877

0.000503308

 
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

Outdata-r100-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

1 (0, 0, 0)

2 (0, 1, 0)
1.49286
0.499949

0.000714213

 
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

Outdata-lx2.5ly7.5lz10.0-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

2 (34, 35, 50)
0.492871
0.499957

0.000714225

 
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
Outdata-m1-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (19, 8, 0)
2.52048e-05
0.00502037

7.2759e-06


Case: -i Specify Input file

-i Input file's image

Input-GaussSphere.png
xy-plane

Input1-GaussSphere.png
yz-plane

Min

Max
Mean
SD

SE

7.97113e-11 (0, 0, 0)

8.32888 (3, 15, 8)
0.223545
0.859713

0.0130319

Output file

Outdata-m1i-mrcImageModelCreate.png
xy-plane

Outdata1-m1i-mrcImageModelCreate.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

8.32888 (64, 34, 0)
0.0220142
0.264693

0.000383612


Case: lx=2.5, ly=7.5, lz=10.0
Outdata-m1lxlylz-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (4, 17, 0)
2.52048e-05
0.00502037

7.2759e-06
Case: radius=100
Outdata-m1radius-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (24, 17, 0)
2.52048e-05
0.00502037

7.2759e-06
Case: n=5
Outdata-n-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (43, 5, 0)
4.2008e-05
0.00648122

9.39307e-06
Case: dz=71
Outdata-m1dz-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (19, 8, 0)
5.04096e-05
0.00709979

1.02896e-05
Case: n=20, dz=7
Outdata-m1ndz-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (34, 4, 0)
0.00302457
0.0549129

7.95839e-05
Case: dphi=20, n=20, dz=7
Outdata-dphi-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1.13578 (58, 16, 99)
0.00302647
0.0549494

7.96368e-05
Case: phi=5, n=20, dz=7
Outdata-m1phi-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1.39997 (64, 34, 99)
0.00303112
0.0550482

7.978e-05
Case: sz=100, ez=300, n=20, dz=7
Outdata-m1szez-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (34, 4, 20)
0.00121823
0.0348819

5.05535e-05

Case: m=2

Outdata-m2-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (17, 17, 0)
6.12245e-06
0.00247435

3.53479e-06

Case: m=3

Outdata-m3-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

40 (42, 40, 0)
0.0537245
1.09497

0.00156424

Case: m=4

Outdata-m4-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

24 (33, 29, 0)
0.0311673
0.613804

0.000876863

Case: m=5

Outdata-m5-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

13 (34, 34, 0)
0.00767959
0.269966

0.000385666

Case: m=6

Outdata-m6-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

2 (33, 3, 0)
0.00551465
0.0803476

0.000114782

Case: m=7

Outdata-m7-mrcImageModelCreate.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

2 (35, 35, 5)
0.384947
0.605556

0.00086508
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