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 |
None | |
Instances |
None | |
Fraction |
1.0 | |
As Points |
True | |
Point Radius |
0.1 | |
Point Material |
None |
Periodic Array
Replicate the trajectory across periodic boundaries.
Outputs
| Description | Socket |
|---|---|
Instances |
Inputs
| Socket | Default | Description |
|---|---|---|
Geometry |
None | |
Update |
True | Update the box lengths and angles with the simulation |
a |
0.0 | |
b |
0.0 | |
c |
0.0 | |
alpha |
0.0 | |
beta |
0.0 | |
gamma |
0.0 | |
X |
3 | Number of images along the a vector |
Y |
3 | Number of images along the b vector |
Z |
3 | Number of images along the c vector |
Periodic Box
Get the box vectors for a trajectory’s periodic simulation box. These vectors can be used to create periodic images of the trajectory
Outputs
| Description | Socket |
|---|---|
A |
|
B |
|
C |
Inputs
| Socket | Default | Description |
|---|---|---|
Update |
True | Update the box lengths and angles with the simulation |
a |
0.0 | |
b |
0.0 | |
c |
0.0 | |
alpha |
0.0 | |
beta |
0.0 | |
gamma |
0.0 |
Periodic Image
Get the location of a single lattice point of the trajectory, based on the box vectors and the chosen lattice indices.
Outputs
| Description | Socket |
|---|---|
Points |
Inputs
| Socket | Default | Description |
|---|---|---|
A |
[0.0, 0.0, 0.0] | |
B |
[0.0, 0.0, 0.0] | |
C |
[0.0, 0.0, 0.0] | |
Image A |
0 | |
Image B |
0 | |
Image C |
0 |
Lattice Grid
Create a grid of lattice points based on the periodic box vectors.
Outputs
| Description | Socket |
|---|---|
Grid |
Inputs
| Socket | Default | Description |
|---|---|---|
A |
[0.0, 0.0, 1.0] | |
B |
[0.0, 0.0, 1.0] | |
C |
[0.0, 0.0, 1.0] | |
X |
3 | Number of images along the a vector |
Y |
3 | Number of images along the b vector |
Z |
3 | Number of images along the c vector |
Starfile Instances
Instance an object onto the given starfile points
Outputs
| Description | Socket |
|---|---|
Instances |
Inputs
| Socket | Default | Description |
|---|---|---|
Points |
None | |
Image |
1 | The ID of the image that should be shown |
Menu |
None | |
Instance |
None | The object that should be placed at each instance |
Material |
None | Material to apply to the resulting geometry |
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 |