Description:
Fundamentally the ParitcleChooser module has the same functionality as the PlaceObjectsInSpace module, but with
the difference, that this module allows you to select a subset of the particles and save it to a new motive-list respectively STAR file or append it to an existing motive-list respectively STAR file.
The structure of the motive-list has dimension (20,NPARTICLES) and is as follows:
| column |
|
| 1 |
Cross-Correlation Coefficient |
| 2 |
x-coordinate in full tomogram |
| 3 |
y-coordinate in full tomogram |
| 4 |
peak number |
| 5 |
not occupied - e.g. use for # of tomogram of extracted particles |
| 8 |
x-coordinate in full tomogram |
| 9 |
y-coordinate in full tomogram |
| 10 |
z-coordinate in full tomogram |
| 11 |
x-shift in subvolume (AFTER rotation) |
| 12 |
y-shift in subvolume (AFTER rotation) |
| 13 |
z-shift in subvolume (AFTER rotation) |
| 14 |
x-shift in subvolume (BEFORE rotation) |
| 15 |
y-shift in subvolume (BEFORE rotation) |
| 16 |
z-shift in subvolume (BEFORE rotation) |
| 17 |
Phi |
| 18 |
Psi |
| 19 |
Theta |
| 20 |
class no |
When loading STAR files, the module will search for the appropriate data block in the file (it will search for a data block where the data item "3D_reconstruction.file_name" is equal to the connected data file in Amira) to visualize the particles. If it does not find an appropriate data block, it will visualize the particles from the first data block.
The structure of a STAR file should at least contain the following data items:
| data_ |
|
|
|
| _{file extension}.3D_reconstruction.id |
{id} |
| _{file extension}.3D_reconstruction.file_name |
{filename} |
| _{file extension}.3D_reconstruction_select |
1 |
| _{file extension}.3D_reconstruction_voxel_size |
{voxel sixe} |
|
|
| loop_ |
|
| _particle.id |
|
| _particle.group_id |
|
| _particle.magnification |
|
| _particle.x |
|
| _particle.y |
|
| _particle.z |
|
| _particle.origin_x |
|
| _particle.origin_y |
|
| _particle.origin_z |
|
| _particle.view_x |
|
| _particle.view_y |
|
| _particle.view_z |
|
| _particle.view_angle |
|
| _particle.fom |
|
| _particle.select |
|
| {List of particle data} |
|
When appending data to a STAR file, the module will search for the appropriate data block in the file (it will search for a data block where the data item "3D_reconstruction.file_name" is equal to the connected data file in Amira). If the module finds the data block, it will update the particle data, otherwise it will append a new data block at the end of the file.
Ports:
Filename for motl
This file chooser defines the path and the filename of the motive-list respectively STAR file.
Choose object
This radio box defines whether the particles should be visualized as spheres or as molecules.
Choose object from file
This file chooser specifies the path and the filename for the molecule.
The port is only visible when the port Choose_object is set to object from file.
Choose colorstyle
This radio box defines whether the color of the particles should be derived from the class number, derived from the
cross-correlation values or set manually.
Choose color for objects
This colormap defines the color of the objects.
The port is only visible when the port Choose_color_style is set to set manually.
Radius
This slider defines the radius of the spheres.
The port is only visible when the port Choose_object is set to sphere.
Values for pixel size
These number fields define the pixel size for either scaling the particle or the volume.
The port is only visible when the port Choose_object is set to object from file.
Visualization
This radio box defines how many particles should be visualized.
Transparency
This slider changes the transparency of all objects.
Threshold for cross-correlation
Only those particles will be visualized which have a cross-correlation value greater than the threshold given by this slider.
The port is only visible when the port Visualization is set to cross-correlation.
Number of particle
This slider defines which particle should be visualized.
The port is only visible when the port Visualization is set to one.
Add or remove particles
This radio box defines whether all or only specified particles are added to the motive-list respectively STAR file or all or specified particles are
removed from the motive-list respectively STAR file. When the port is set to idle nothing will happen when a particle is clicked.
Create new motl or append
This radio box determines whether the chosen particles will be appended in an existing motive-list respectively STAR file or saved in a new one.
Filename for saving motl
This file chooser defines the path to and the filename of the motive-list respectively STAR file where the particles will be saved.
Save motl
When this button is pressed, the particles will be saved in the motive-list respectively STAR file.
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