mrc2Dto3D
mrc2Dto3D is a command Eos to 3D images from 2D images which is an electron micrographs. From the angle information of the particle cut out, to reconstruct a three-dimensional structure using a back projection technique. The output is a 3d file dsn6, it is possible to display (such as chimera or VMD) molecule viewer density map.
Contents
List of option
Main option
The setting of the mode and each parameter.
| Option | Essential/Optional | Description | Default |
|---|---|---|---|
| -i | Optional | Input: mrcImage[2DSet] | NULL |
| -I | Optional | InputDataFile | NULL |
| -each | Optional | Read when needed files one by one | |
| -o | Essential | Output: mrcImage[3D] | NULL |
| -O | Optional | OutputDataFile[2DMulti] | NULL |
| -single | Optional | SingleTiltMode | 1 |
| -InterpolationMode | Optional | Interpolation Mode | 1 |
| -Double | Optional | DoubleTiltMode | |
| -DoubleCounter | Optional | Only when setting -Double DoubleCounter |
NULL |
| -CounterThreshold | Optional | Only when setting -Double Threshold of the Valley of the waveform |
1e-6 |
| -CounterThresholdMode | Optional | Only when setting -Double Mode of threshold of the Valley of the waveform |
0 |
| -WeightMode | Optional | Only when setting -Double Mode of the center of gravity |
0 |
| -thicknessWeight | Optional | Only when setting -Double The depth of the center of gravity |
|
| -Sub | Optional | Only when setting -Double SubSampling: [pixel] |
1 |
| -PlusXrot | Optional | The 180 ° rotation of the x-axis for rasmol | |
| -SIRT | Optional | SIRT (Simultaneous Iterative Reconstruction Technique) | |
| -max | Optional | Only when setting -SIRT Max Value setting of SIRT |
30 |
| -rms | Optional | Only when setting -SIRT RMS (root mean square) setting of SIRT |
1.0 |
| -CTF | Optional | Only when setting -SIRT CTF information file setting |
NULL |
| -m | Optional | Mode | 0 |
| -h | Optional | Help |
-m details
Setting of the projected image mode.
| Value | Description |
|---|---|
| 0 | Simple back projection |
| 1 | Filtered back projection |
| 2 | Weighted back projection |
-single details
Setting of the tilt axis.
| Value | Description |
|---|---|
| 0 | The parallel to the x-axis tilt axis |
| 1 | The parallel to the y-axis tilt axis |
-WeightMode details
Setting of weights when calculating.
| Value | Description |
|---|---|
| 1 | Real space: Circle(same density) |
| 2 | Real space: Circle(weighted density) |
| 3 | Real space: Square(weighted density) |
| 4 | Fourier space: Plane(same density) -CounterThreshold 0.5 |
| 5 | Fourier space: Plane(Linear Gradient)-CounterThreshold 0.5 |
| 6 | Fourier space: Plane(Cosine Gradient) Current Recommende using -CounterThreshold 0.5 |
-InterpolationMode details
Setting of Interpolation Mode.
| Value | Description |
|---|---|
| 0 | Nearest neighbor method |
| 1 | Bi-linear interpolation method |
| 2 | Cubic convolution method |
| 3 | Polynomial interpolation method |
-I format
filename0 RotationOrder0 rot1 rot2 rot3 filename1 RotationOrder1 rot1 rot2 rot3 ・ ・ ・
Rotation Order details
1st digit: Setting the rotation axis of the first 2nd digit: Setting the order-1 of the rotation axis O: Order Z -> Y-> X E: Order Z -> X-> Y 3rd digit: Setting the order-2 of the rotation axis Y: Keep the order N: Reverse the order 4th digit: Setting rotation method S: Rotate the object N: Move the coordinates
Execution example
-i example
Is shown in Fig.1 the file that was used in the option -i as a specific example. Details of these images are as follows.
Min 0 Max 0.175 Mean 0.00302838 SD 0.0129759 SE 8.75794e-06
Output result is Fig.2 followed. Details are as follows.
Min 0 Max 0.0872652 Mean 0.00352428 SD 0.00653417 SE 9.13179e-06
Fig.1-1:XY-plane of the input image
Fig.1-2:ZX-plane of the input image
Fig.2:Output image
-I example
For more information about the file that was used in the option -I. The input file is as follows.
a000-2a.orgmrc YOYS 0 60 0
a004-2a.orgmrc YOYS 0 56 0
a008-2a.orgmrc YOYS 0 52 0
a012-2a.orgmrc YOYS 0 48 0
a016-2a.orgmrc YOYS 0 44 0
a020-2a.orgmrc YOYS 0 40 0
a024-2a.orgmrc YOYS 0 36 0
・
・
・
Fig.3 shows a portion of the input image. In the same object a004-2.orgmrc and a000-2.orgmrc, it is an image tilt angle is different. Details of each are as follows.
a000-2.orgmrc: Min 0 Max 37.8872 Mean 0.833407 SD 4.20486 SE 0.0420486
a004-2.orgmrc: Min 0 Max 38.0379 Mean 0.833354 SD 4.19112 SE 0.0419112
Fig.3-1:a000-2.orgmrc Image
Fig.3-2:a004-2.orgmrc Image
-single example
Tilt axis this is the y-axis from the details of the input file.
Min 0 Max 33.7425 Mean 0.92622 SD 2.73412 SE 0.00273412
Fig.4-1:XY-plane of the input image
Fig.4-2:YZ-plane
Fig.4-3:ZX-plane
-Double example
The combination option -WeightMode, -CounterThreshhold.
-CounterThreshhold is 2
WeightMode: 1
 |
Min Max |
-24.3363 115.7 |
 |
Min Max |
-23.6896 117.242 |
 |
Min Max |
-23.6896 117.242 |
 |
Min Max |
-40.5762 174.198 |
 |
Min Max |
-41.7929 185.856 |
 |
Min Max |
-43.5065 190.759 |
With option -CounterThresholdMode
Executing at the option -WeightMode=1, -CounterThreshhold=2.
 |
Min Max |
-24.3363 115.7 |
 |
Min Max |
-20.1632 113.527 |
-InterpolationMode example
Executing at the option -WeightMode=1, -CounterThreshhold=2.
 |
Min Max |
-24.6593 117.022 |
 |
Min Max |
-24.3363 115.7 |
 |
Min Max |
-26.0299 118.253 |
 |
Min Max |
-40640.8 209412 |
-SIRT example
Executing of SIRT.
Option -max,-rms are default value, -WeightMode=1, -CounterThreshhold=2.
 |
Min Max |
-725.47 2563.64 |
 |
Min Max |
-234.062 575.77 |
-m example
 |
Min Max |
0 30.514 |
 |
Min Max |
-54.8893 125.857 |
