mrcImageModelCreate - Revision history

Kinoshita: /* Case: -i Specify Input file */

2014-09-10T01:12:04Z

‎Case: -i Specify Input file

Kinoshita: /* Case: No other settings */

2014-09-10T01:05:39Z

‎Case: No other settings

Kinoshita: /* Case: lx=2.5, ly=7.5, lz=10.0 */

2014-09-10T01:03:43Z

‎Case: lx=2.5, ly=7.5, lz=10.0

Kinoshita: /* Option -m */

2014-09-10T00:58:55Z

‎Option -m

Kinoshita: /* Case: m=1, nx=69, ny=69 */

2014-09-10T00:45:07Z

‎Case: m=1, nx=69, ny=69

Kinoshita: Created page with "'''mrcImageModelCreate''' is Eos's Command that creates the model image. == List of option == === Main option === ..."
2014-07-28T00:57:39Z
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>..."
New page
'''mrcImageModelCreate''' is [[Eos]]'s [[Command]] that creates the model image.

== List of option ==
=== Main option ===
<table border="1">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-i</td>
<td>Optional</td>
<td>Input</td>
<td>NULL</td>
</tr>
<tr>
<td>-nx</td>
<td>Optional</td>
<td>Real length = nx * lx</td>
<td>70</td>
</tr>
<tr>
<td>-ny</td>
<td>Optional</td>
<td>Real length = ny * ly</td>
<td>70</td>
</tr>
<tr>
<td>-nz</td>
<td>Optional</td>
<td>Real length = nz * lz</td>
<td>100</td>
</tr>
<tr>
<td>-r</td>
<td>Optional</td>
<td>radius[pixel]</td>
<td>1</td>
</tr>
<tr>
<td>-lx</td>
<td>Optional</td>
<td>Pixel Size[Angstrom]</td>
<td>5.0</td>
</tr>
<tr>
<td>-ly</td>
<td>Optional</td>
<td>Pixel Size[Angstrom]</td>
<td>5.0</td>
</tr>
<tr>
<td>-lz</td>
<td>Optional</td>
<td>Pixel Size[Angstrom]</td>
<td>5.0</td>
</tr>
<tr>
<td>-radius</td>
<td>Optional</td>
<td>filament radius [A]</td>
<td>150</td>
</tr>
<tr>
<td>-n</td>
<td>Optional</td>
<td>n-helix</td>
<td>3</td>
</tr>
<tr>
<td>-dz</td>
<td>Optional</td>
<td>pitch [A]</td>
<td>143</td>
</tr>
<tr>
<td>-dphi</td>
<td>Optional</td>
<td>rotation angle [degree]</td>
<td>40</td>
</tr>
<tr>
<td>-phi</td>
<td>Optional</td>
<td>rotation angle in the same level [degree]</td>
<td>120</td>
</tr>
<tr>
<td>-sz</td>
<td>Optional</td>
<td>start z [A]</td>
<td>0</td>
</tr>
<tr>
<td>-ez</td>
<td>Optional</td>
<td>end z [A]</td>
<td>500</td>
</tr>
<tr>
<td>-sphi</td>
<td>Optional</td>
<td>start angle [degree]</td>
<td>0</td>
</tr>
<tr>
<td>-sphi2</td>
<td>Optional</td>
<td>start angle 2 [degree]</td>
<td>40</td>
</tr>
<tr>
<td>-inMode</td>
<td>Optional</td>
<td>inMode</td>
<td>0</td>
</tr>
<tr>
<td>-units</td>
<td>Optional</td>
<td>units number</td>
<td>9</td>
</tr>
<tr>
<td>-fm</td>
<td>Optional</td>
<td>formation</td>
<td>0</td>
</tr>
<tr>
<td>-c</td>
<td>Optional</td>
<td>ConfigurationFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Mode</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Circle(a right cylinder:3D) and Triangle(a trigonal prism:3D) 
Optional argument : -nx -ny -nz -r </td>
</tr>
<tr>
<td>1</td>
<td>Thick Filaments 
<pre>
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
</pre></td>
</tr>
<tr>
<td>2</td>
<td>Dot(2D)</td>
</tr>
<tr>
<td>3</td>
<td>Projection of 2 Sphere and 2 circle for 2D 
Optional argument : -nx -ny </td>
</tr>
<tr>
<td>4</td>
<td>Another Projection of 2 Sphere and 2 circle for 2D 
Optional argument : -nx -ny </td>
</tr>
<tr>
<td>5</td>
<td>Another Projection of 2 Sphere for 2D 
Optional argument : -nx -ny </td>
</tr>
<tr>
<td>6</td>
<td>SheppLogan 2D 
Optional argument : -nx -ny </td>
</tr>
<tr>
<td>7</td>
<td>SheppLogan 3D 
Optional argument : -nx -ny -nz </td>
</tr>
</table>

== Execution example ==
=== Example of options only essential ===
<table>
<tr>
<td>[[File:Outdata-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
2 (34, 35, 50) 
0.492871 
0.499957 
0.000714225 
</td>
</tr>
</table>

<pre>
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)
</pre>

=== Option -nx, -ny, -nz===
====Case: nx=50, ny=100, nz=150====
<table>
<tr>
<td>[[File:Outdata-nx50ny100nz150-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
2 (25, 50, 74) 
0.745009 
0.435877 
0.000503308 
</td>
</tr>
</table>

<pre>
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)
</pre>

=== Option -r===
====Case: r=100====
<table>
<tr>
<td>[[File:Outdata-r100-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>1 (0, 0, 0) 
2 (0, 1, 0) 
1.49286 
0.499949 
0.000714213 
</td>
</tr>
</table>

<pre>
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)
</pre>

=== Option -lx, -ly, -lz===
====Case: lx=2.5, ly=7.5, lz=10.0====
<table>
<tr>
<td>[[File:Outdata-lx2.5ly7.5lz10.0-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
2 (34, 35, 50) 
0.492871 
0.499957 
0.000714225 
</td>
</tr>
</table>

<pre>
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)
</pre>

=== Option -m===
====Case: m=1, nx=69, ny=69====
=====Case: No other settings=====
<table>
<tr>
<td>[[File:Outdata-m1-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (19, 8, 0) 
2.52048e-05 
0.00502037 
7.2759e-06 
</td>
</tr>
</table>

=====Case: lx=2.5, ly=7.5, lz=10.0=====
<table>
<tr>
<td>[[File:Outdata-m1lxlylz-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (4, 17, 0) 
2.52048e-05 
0.00502037 
7.2759e-06 
</td>
</tr>
</table>

=====Case: radius=100=====
<table>
<tr>
<td>[[File:Outdata-m1radius-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (24, 17, 0) 
2.52048e-05 
0.00502037 
7.2759e-06 
</td>
</tr>
</table>

=====Case: n=5=====
<table>
<tr>
<td>[[File:Outdata-n-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (43, 5, 0) 
4.2008e-05 
0.00648122 
9.39307e-06 
</td>
</tr>
</table>

=====Case: dz=71=====
<table>
<tr>
<td>[[File:Outdata-m1dz-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (19, 8, 0) 
5.04096e-05 
0.00709979 
1.02896e-05 
</td>
</tr>
</table>

=====Case: n=20, dz=7=====
<table>
<tr>
<td>[[File:Outdata-m1ndz-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (34, 4, 0) 
0.00302457 
0.0549129 
7.95839e-05 
</td>
</tr>
</table>

=====Case: dphi=20, n=20, dz=7=====
<table>
<tr>
<td>[[File:Outdata-dphi-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1.13578 (58, 16, 99) 
0.00302647 
0.0549494 
7.96368e-05 
</td>
</tr>
</table>

=====Case: phi=5, n=20, dz=7=====
<table>
<tr>
<td>[[File:Outdata-m1phi-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1.39997 (64, 34, 99) 
0.00303112 
0.0550482 
7.978e-05 
</td>
</tr>
</table>

=====Case: sz=100, ez=300, n=20, dz=7=====
<table>
<tr>
<td>[[File:Outdata-m1szez-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (34, 4, 20) 
0.00121823 
0.0348819 
5.05535e-05 
</td>
</tr>
</table>

====Case: m=2====
<table>
<tr>
<td>[[File:Outdata-m2-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (17, 17, 0) 
6.12245e-06 
0.00247435 
3.53479e-06 
</td>
</tr>
</table>

====Case: m=3====
<table>
<tr>
<td>[[File:Outdata-m3-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
40 (42, 40, 0) 
0.0537245 
1.09497 
0.00156424 
</td>
</tr>
</table>

====Case: m=4====
<table>
<tr>
<td>[[File:Outdata-m4-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
24 (33, 29, 0) 
0.0311673 
0.613804 
0.000876863 
</td>
</tr>
</table>

====Case: m=5====
<table>
<tr>
<td>[[File:Outdata-m5-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
13 (34, 34, 0) 
0.00767959 
0.269966 
0.000385666 
</td>
</tr>
</table>

====Case: m=6====
<table>
<tr>
<td>[[File:Outdata-m6-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
2 (33, 3, 0) 
0.00551465 
0.0803476 
0.000114782 
</td>
</tr>
</table>

====Case: m=7====
<table>
<tr>
<td>[[File:Outdata-m7-mrcImageModelCreate.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
2 (35, 35, 5) 
0.384947 
0.605556 
0.00086508 
</td>
</tr>
</table>

Option

@@ Line 410: / Line 410: @@
 				Mean<br>
 				SD<br>
-				SE<br></p>
+				SE<br>
 			</td>
 			<td><p align="left">7.97113e-11 (0, 0, 0)<br>
@@ Line 416: / Line 417: @@
 .223545<br>
 .859713<br>
-.0130319<br></p>
+.0130319<br>
 			</td>
 		</tr>
@@ Line 434: / Line 436: @@
 				Mean<br>
 				SD<br>
-				SE<br></p>
+				SE<br>
 			</td>
 			<td><p align="left">0 (0, 0, 0)<br>
@@ Line 440: / Line 443: @@
 .0220142<br>
 .264693<br>
-.000383612<br></p>
+.000383612<br>
 			</td>
 		</tr>
 	</table>
 <br>

@@ Line 382: / Line 382: @@
 				Mean<br>
 				SD<br>
-				SE<br></p>
+				SE<br>
 			</td>
 			<td><p align="left">0 (0, 0, 0)<br>
@@ Line 388: / Line 389: @@
 .52048e-05<br>
 .00502037<br>
-.2759e-06<br></p>
+.2759e-06<br>
 			</td>
 		</tr>

@@ Line 457: / Line 457: @@
 				Mean<br>
 				SD<br>
-				SE<br></p>
+				SE<br>
 			</td>
 			<td><p align="left">0 (0, 0, 0)<br>
@@ Line 463: / Line 464: @@
 .52048e-05<br>
 .00502037<br>
-.2759e-06<br></p>
+.2759e-06<br>
 			</td>
 		</tr>
 	</table>
 =====Case: radius=100=====

@@ Line 372: / Line 372: @@
 	<table>
 		<tr>
-			<td>[[File:Outdata-m1-mrcImageModelCreate.png]]</td>
+			<td><p align="Center">[[File:Outdata1-m1-mrcImageModelCreate.png]]<br>
 			<td><p align="left">Min<br>
 				Max<br>
@@ Line 442: / Line 447: @@
 	<table>
 		<tr>
-			<td>[[File:Outdata-m1lxlylz-mrcImageModelCreate.png]]</td>
+			<td><p align="Center">[[File:Outdata1-m1lxlylz-mrcImageModelCreate.png]]<br>
 			<td><p align="left">Min<br>
 				Max<br>
@@ Line 461: / Line 471: @@
 	<table>
 		<tr>
-			<td>[[File:Outdata-m1radius-mrcImageModelCreate.png]]</td>
+			<td><p align="Center">[[File:Outdata1-m1radius-mrcImageModelCreate.png]]<br>
 			<td><p align="left">Min<br>
 				Max<br>
@@ Line 480: / Line 495: @@
 	<table>
 		<tr>
-			<td>[[File:Outdata-n-mrcImageModelCreate.png]]</td>
+			<td><p align="Center">[[File:Outdata1-n-mrcImageModelCreate.png]]<br>
 			<td><p align="left">Min<br>
 				Max<br>
@@ Line 499: / Line 519: @@
 	<table>
 		<tr>
-			<td>[[File:Outdata-m1dz-mrcImageModelCreate.png]]</td>
+			<td><p align="Center">[[File:Outdata1-m1dz-mrcImageModelCreate.png]]<br>
 			<td><p align="left">Min<br>
 				Max<br>
@@ Line 518: / Line 543: @@
 	<table>
 		<tr>
-			<td>[[File:Outdata-m1ndz-mrcImageModelCreate.png]]</td>
+			<td><p align="Center">[[File:Outdata1-m1ndz-mrcImageModelCreate.png]]<br>
 			<td><p align="left">Min<br>
 				Max<br>
@@ Line 537: / Line 567: @@
 	<table>
 		<tr>
-			<td>[[File:Outdata-dphi-mrcImageModelCreate.png]]</td>
+			<td><p align="Center">[[File:Outdata1-dphi-mrcImageModelCreate.png]]<br>
 			<td><p align="left">Min<br>
 				Max<br>
@@ Line 556: / Line 591: @@
 	<table>
 		<tr>
-			<td>[[File:Outdata-m1phi-mrcImageModelCreate.png]]</td>
+			<td><p align="Center">[[File:Outdata1-m1phi-mrcImageModelCreate.png]]<br>
 			<td><p align="left">Min<br>
 				Max<br>
@@ Line 575: / Line 615: @@
 	<table>
 		<tr>
-			<td>[[File:Outdata-m1szez-mrcImageModelCreate.png]]</td>
+			<td><p align="Center">[[File:Outdata1-m1szez-mrcImageModelCreate.png]]<br>
 			<td><p align="left">Min<br>
 				Max<br>

@@ Line 387: / Line 387: @@
 		</tr>
 	</table>
 =====Case: lx=2.5, ly=7.5, lz=10.0=====
@@ Line 538: / Line 589: @@
 			</td>
 		</tr>
 	</table>
 ====Case: m=2====