Select
Separate Atoms
Separate the input atoms intwo the Atoms
and Inverted
based on the input selection. For simply styling this can the same as inputting the selecting directly into the Style node. The one additional output for this node is the Index
field, which is the index of the atom in the original structure before the selection happened and potentially changed it’s index
Inputs
Name | Type | Description | Default |
---|---|---|---|
Atoms | Geometry |
Atomic geometry that contains vertices and edges | None |
Selection | Bool |
Selection field for which atoms to separate | True |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Atoms | Geometry |
The selected atoms | None |
Inverted | Geometry |
The inverse of the calculated selection | None |
Index | Int |
Index of the atoms before they were separated | None |
Separate Polymers
Separate the input atomic geometry into it’s different polymers or Protein
, Nucleic Acid
and other
.
Inputs
Name | Type | Description | Default |
---|---|---|---|
Atoms | Geometry |
Atomic geometry that contains vertices and edges | None |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Peptide | Geometry |
None | |
Nucleic | Geometry |
None | |
Other | Geometry |
None |
Select Chain
Select single or multiple of the different chains. Creates a selection based on the chain_id
attribute.
Inputs
Name | Type | Description | Default |
---|---|---|---|
Chain A | Bool |
Select the atoms in Chain A | True |
Chain B | Bool |
Select the atoms in Chain B | True |
Chain … | Bool |
Select the atoms in Chain … | True |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Entity
Select single or multiple of the different entities. Creates a selection based on the entity_id
attribute.
Inputs
Name | Type | Description | Default |
---|---|---|---|
Entity A | Bool |
Select the atoms in Entity A | True |
Entity B | Bool |
Select the atoms in Entity B | True |
Entity … | Bool |
Select the atoms in Entity … | True |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Ligand
Select single or multiple of the different ligands.
Inputs
Name | Type | Description | Default |
---|---|---|---|
Ligand A | Bool |
Select the atoms in Ligand A | True |
Ligand B | Bool |
Select the atoms in Ligand B | True |
Ligand … | Bool |
Select the atoms in Ligand … | True |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Segment
Output a selection based on the segment_id
that is present in some MD trajectories
Inputs
Name | Type | Description | Default |
---|---|---|---|
Segment A | Bool |
Select the atoms in Ligand A | True |
Segment B | Bool |
Select the atoms in Ligand B | True |
Segment … | Bool |
Select the atoms in Ligand … | True |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Atomic Number
Select points based on their atomic_number
attribute, corresponding to the element’s atomic number. Useful for selecting single elements quickly
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
atomic_number | Int |
Create a selection based on the inputted atomic number. | None |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Element
Select points for the first 80 elemnts of the preiodic table, via a boolean input. Elements are grouped into panels of 20 each for orgnaisation and convenience
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
H | Bool |
Select the element H | False |
He | Bool |
Select the element He | False |
Li | Bool |
Select the element Li | False |
Be | Bool |
Select the element Be | False |
B | Bool |
Select the element B | False |
C | Bool |
Select the element C | False |
N | Bool |
Select the element N | False |
O | Bool |
Select the element O | False |
F | Bool |
Select the element F | False |
Ne | Bool |
Select the element Ne | False |
Na | Bool |
Select the element Na | False |
Mg | Bool |
Select the element Mg | False |
Al | Bool |
Select the element Al | False |
Si | Bool |
Select the element Si | False |
P | Bool |
Select the element P | False |
S | Bool |
Select the element S | False |
Cl | Bool |
Select the element Cl | False |
Ar | Bool |
Select the element Ar | False |
K | Bool |
Select the element K | False |
Ca | Bool |
Select the element Ca | False |
Sc | Bool |
Select the element Sc | False |
Ti | Bool |
Select the element Ti | False |
V | Bool |
Select the element V | False |
Cr | Bool |
Select the element Cr | False |
Mn | Bool |
Select the element Mn | False |
Fe | Bool |
Select the element Fe | False |
Co | Bool |
Select the element Co | False |
Ni | Bool |
Select the element Ni | False |
Cu | Bool |
Select the element Cu | False |
Zn | Bool |
Select the element Zn | False |
Ga | Bool |
Select the element Ga | False |
Ge | Bool |
Select the element Ge | False |
As | Bool |
Select the element As | False |
Se | Bool |
Select the element Se | False |
Br | Bool |
Select the element Br | False |
Kr | Bool |
Select the element Kr | False |
Rb | Bool |
Select the element Rb | False |
Sr | Bool |
Select the element Sr | False |
Y | Bool |
Select the element Y | False |
Zr | Bool |
Select the element Zr | False |
Nb | Bool |
Select the element Nb | False |
Mo | Bool |
Select the element Mo | False |
Tc | Bool |
Select the element Tc | False |
Ru | Bool |
Select the element Ru | False |
Rh | Bool |
Select the element Rh | False |
Pd | Bool |
Select the element Pd | False |
Ag | Bool |
Select the element Ag | False |
Cd | Bool |
Select the element Cd | False |
In | Bool |
Select the element In | False |
Sn | Bool |
Select the element Sn | False |
Sb | Bool |
Select the element Sb | False |
Te | Bool |
Select the element Te | False |
I | Bool |
Select the element I | False |
Xe | Bool |
Select the element Xe | False |
Cs | Bool |
Select the element Cs | False |
Ba | Bool |
Select the element Ba | False |
La | Bool |
Select the element La | False |
Ce | Bool |
Select the element Ce | False |
Pr | Bool |
Select the element Pr | False |
Nd | Bool |
Select the element Nd | False |
Pm | Bool |
Select the element Pm | False |
Sm | Bool |
Select the element Sm | False |
Eu | Bool |
Select the element Eu | False |
Gd | Bool |
Select the element Gd | False |
Tb | Bool |
Select the element Tb | False |
Dy | Bool |
Select the element Dy | False |
Ho | Bool |
Select the element Ho | False |
Er | Bool |
Select the element Er | False |
Tm | Bool |
Select the element Tm | False |
Yb | Bool |
Select the element Yb | False |
Lu | Bool |
Select the element Lu | False |
Hf | Bool |
Select the element Hf | False |
Ta | Bool |
Select the element Ta | False |
W | Bool |
Select the element W | False |
Re | Bool |
Select the element Re | False |
Os | Bool |
Select the element Os | False |
Ir | Bool |
Select the element Ir | False |
Pt | Bool |
Select the element Pt | False |
Au | Bool |
Select the element Au | False |
Hg | Bool |
Select the element Hg | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Res Name
Select points based on their res_id
attribute for different peptide or nucleic acid residue names. Inputs are arranged alphabetically and in panels of Protein, RNA and DNA for layout
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
ALA | Bool |
Select the residue ALA | False |
ARG | Bool |
Select the residue ARG | False |
ASN | Bool |
Select the residue ASN | False |
ASP | Bool |
Select the residue ASP | False |
CYS | Bool |
Select the residue CYS | False |
GLU | Bool |
Select the residue GLU | False |
GLN | Bool |
Select the residue GLN | False |
GLY | Bool |
Select the residue GLY | False |
HIS | Bool |
Select the residue HIS | False |
ILE | Bool |
Select the residue ILE | False |
LEU | Bool |
Select the residue LEU | False |
LYS | Bool |
Select the residue LYS | False |
MET | Bool |
Select the residue MET | False |
PHE | Bool |
Select the residue PHE | False |
PRO | Bool |
Select the residue PRO | False |
SER | Bool |
Select the residue SER | False |
THR | Bool |
Select the residue THR | False |
TRP | Bool |
Select the residue TRP | False |
TYR | Bool |
Select the residue TYR | False |
VAL | Bool |
Select the residue VAL | False |
A | Bool |
Select the residue A | False |
C | Bool |
Select the residue C | False |
G | Bool |
Select the residue G | False |
T | Bool |
Select the residue T | False |
rA | Bool |
Select the residue rA | False |
rC | Bool |
Select the residue rC | False |
rG | Bool |
Select the residue rG | False |
rU | Bool |
Select the residue rU | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Res ID
Select a atoms based on their res_id
number.
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Res ID | Int |
A single res_id selection |
None |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Res ID Range
Select multiple residues by specifying a Min and a Max, defining a range that includes or excludes based on the res_id
number.
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Min | Int |
Minimum of a res_id range selection |
None |
Max | Int |
Maximum of a res_id range selection |
None |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Res ID
Create a more complex selection for the res_id
field, by specifying multiple ranges and potential single res_id
numbers. This node is built uniquely each time, to the inputs will look different for each user. In the example below, residues 10 & 15 are selected, as well as residues between and including 20-100. The node was created by inputting 10, 15, 20-100
into the node creation field.
Inputs
Name | Type | Description | Default |
---|---|---|---|
res_id | Int |
A single res_id selection |
None |
res_id | Int |
A single res_id selection |
None |
res_id: Min | Int |
Minimum of a res_id range selection |
None |
res_id: Max | Int |
Maximum of a res_id range selection |
None |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Attribute
Select atoms that have true for the given attribute name.
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Name | String |
is_peptide |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Is Peptide
Outputs a selection for all of the points in a peptide
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Is Nucleic
Outputs a selection for all of the points in a nucleic acid molecule
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Is Lipid
Select the atoms involved in lipid molecules.
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Is Solvent
Select the atoms that are part of the solvent.
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Is Alpha Carbon
Outputs a selection for all of the points that are alpha carbons (CA) in the structure
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Is Backbone
Outputs a selection for the backbone atoms of a peptide or nucleic acid polymer. Peptide backbone includes the peptide oxygen and the alpha carbon as part of the backbone
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Is Side Chain
Outputs a selection for the side chain atoms of a peptide or nucleic acid polymer. Peptide side chain can optionally include or exclude the alpha carbon CA of the side chain
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Include CA | Bool |
Include the alpha carbon as part of the side chain | True |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Is Helix
Outputs a selection for points that are part of a helix. The sec_struct
attribute must exist, either imported from the file or computed with the DSSP
node
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Is Sheet
Outputs a selection for points that are part of a sheet. The sec_struct
attribute must exist, either import from the file or computed with the DSSP
node
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Is Loop
Outputs a selection for those points in a peptide which are not part of any secondary structure (loop or helix)
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Bonded
Based on an initial selection, finds atoms which are within a certain number of bonds of this selection. Output can include or excluded the original selection.
Inputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
Selection of atoms to apply this node to | False |
Depth | Int |
Number of bonds to expand the selection by | None |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Bonded | Bool |
Expanded Selection that excludes the original selection | False |
Select Res Whole
Expand the given selection to include a whole residue, if a single atom in that residue is selected. Useful for when a distance or proximity selection includes some of the residue and you wish to include all of the residue.
Inputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
Selection of atoms to apply this node to | False |
Expand | Bool |
Whether to expand the selection to the whole residue if at least one atom is selected | True |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Select Cube
Create a selection that is inside the Empty_Cube
object. When this node is first created, an empty object called Empty_Cube
should be created. You can always create additional empty objects through the add menu, to use a different object. The rotation and scale of the object will be taken into account for the selection.
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Object | Object |
The position, rotation and scale from this Object will be used for the distance calculation for the selection. By default an Empty object is used, but any object can be used in principle | <bpy_struct, Object("select_cube") at 0x7f31c5aea820> |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Sphere
Create a selection that is within a spherical radius of an object, based on that object’s scale. By default an empty object called Empty_Sphere
is created. You can use other objects or create a new empty to use. The origin point for the object will be used, which should be taken in to account when using molecules. Use MN_select_proximity
for selections which are within a certain distance of a selection of atoms instead of a single origin point.
Inputs
Name | Type | Description | Default |
---|---|---|---|
And | Bool |
The resulting selection must overlap with this input selection | True |
Or | Bool |
The resulting selection can be calculated from this node or be from this input selection | False |
Object | Object |
The position from this Object will be used for the distance calculation for the selection. By default an Empty object is used, but any object can be used in principle | <bpy_struct, Object("select_sphere") at 0x7f31c5aead20> |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |
Select Proximity
Create a selection based on the proximity to the Target Atoms of the input. A sub-selection of the Target atoms can be used if the Subset
input is used. You can expand the selection to include an entire residue if a single atom in that residue is selected, by setting Expand
to True
. In the example below, the Style Atoms
is being applied to a selection, which is being calculated from the proximity of atoms to specific chains. As the cutoff for the selection is changed, it includes or excludes more atoms. The Whole Residue
option also ensures that entire residues are shown.
Inputs
Name | Type | Description | Default |
---|---|---|---|
Target Atoms | Geometry |
The atoms to measure the distance from. | None |
Subset | Bool |
Subset of input atoms to use for proximity calculation | True |
Expand | Bool |
Include an entire residue if even a single atom is within the threshold | False |
Distance (A) | Float |
Cutoff distance for the selection in Angstroms | 5.0 |
Outputs
Name | Type | Description | Default |
---|---|---|---|
Selection | Bool |
The calculated selection | False |
Inverted | Bool |
The inverse of the calculated selection | False |