Ensemble
MN_assembly_
Creates a biological assembly by applying rotation and translation matrices to individual chains in the structure. It is created on an individual molecule basis, if assembly instructions are detected when imported. ::: callout-caution Style Spheres requires the material to be set again after the assembly node, as the material is currently lost when joining multiple point clouds. :::
Outputs
| Description | Socket |
|---|---|
Assembled Chain Instances |
Inputs
| Socket | Default | Description |
|---|---|---|
Geometry |
None | Any geometry to separate into chains and instance |
Rotation |
1.0 | Amount to apply the rotation of the matrix |
Translation |
1.0 | Amount to apply the translation of the matrix |
assembly_id |
1 | Which biological assembly to create |
MN_assembly_center
Move an instanced assembly to the world origin. Some structures are not centred on the world origin, so this node can reset them to the world origin for convenient rotation and translation and animation.
Outputs
| Description | Socket |
|---|---|
| The translated assembly | Assembly Instances |
| The old centre point of the assembly | Old Centre |
| The transformation that was applied to the assembly | Transform Vector |
Inputs
| Socket | Default | Description |
|---|---|---|
Assembly Instances |
None | The instances of an assembly, the result of MN_assembly |
Center |
True | Whether to center the assembly |
Translation |
[0.0, 0.0, 0.0] | Additional translation to apply to the centered assembly |
Ensemble Instance
Instance the items of an ensemble onto the given points
Outputs
| Description | Socket |
|---|---|
Instances |
Inputs
| Socket | Default | Description |
|---|---|---|
Points |
None | |
Selection |
True | Selection of atoms to apply this node to |
Selection Type |
Simple | |
Instances |
None | |
Fraction |
1.0 | |
As Points |
True | |
Point Radius |
0.1 | |
Point Material |
None |
Starfile Instances
Instance an object onto the given starfile points
Outputs
| Description | Socket |
|---|---|
Instances |
Inputs
| Socket | Default | Description |
|---|---|---|
Geometry |
None | |
Molecule |
None | The object that should be placed at each instance |
Image |
1 | The ID of the image that should be shown |
Simplify |
False | Place axes instead of Molecule on each instance |
Material |
None | Material to apply to the resulting geometry |
Show Micrograph |
False | Show the micrograph in addition to the instances |
Micrograph::Image |
None | The image object used for the micrograph (should be set automatically) |
Micrograph Pixelsize |
-1.0 | Pixelsize of the micrograph (enter a negative number to use value from starfile) |
Micrograph Z |
-10.0 | Position of the micrograph along the Z axis |
Brightness |
0.5 | Adjust micrograph brightness |
Contrast |
1.0 | Adjust micrograph contrast |
Rotation RELION
A rotation calculated from relevant columns of a RELION .star file
Outputs
| Description | Socket |
|---|---|
Is Valid |
|
Rotation |
Rotation cisTEM
A rotation calculated from relevant columns of a cisTEM .star file
Outputs
| Description | Socket |
|---|---|
Is Valid |
|
Rotation |