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 0x7f6edace0320>

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 0x7f6edace0820>

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