Description:
The PlaceObjectsInSpace module is a tool to visualize the particles of a motive-list or a STAR file. The particles can either be
visualized as a sphere or as a molecule which is given through a filename. If this filename has the extension ".star", the file will be read as a STAR file and the file content will be converted to the structure of a motive-list. If the extension differs form ".star", the file will be read as a motive-list. The particular objects are placed at the position,
rotated by phi, psi and theta and are scaled according to the entries in the motive-list. The color of the objects can be set manually,
derived from the class number of the objects or derived from the cross correlation value of the object.
Furthermore it is possible to visualize all objects, only one, none or only those objects which have a cross correlation value higher
than a given threshold.
Besides that, it is possible to label the objects with any value of the motive-list as well as the entry number in the motive-list.
The objects will be visualized when the Apply button is pressed.
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} |
|
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.
Specular Intensity
This slider changes the intensity of the specular highlights of all objects.
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.
Label particle with
This radio box defines which value, if any, should be used for labeling the particles.
Column for Labeling
This slider defines the value of the motive-list which will be used for labeling.
The port is only visible when the port Label_particle_with is set to MOTL row.
Text size
This slider defines the font size of the label.
The port is only visible when the port Label_particle_with is set to MOTL order or to MOTL row.
Choose text colorstyle
This radio box defines whether the text color should be derived from the particle color or set manually.
The port is only visible when the port Label_particle_with is set to MOTL order or to MOTL row.
Choose text color
This colormap defines the text color.
The port is only visible when the port Choose_text_colorstyle is set to set manually.
| 
