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

Outputs

Description Socket
The selected atoms Atoms
The inverse of the calculated selection Inverted
Index of the atoms before they were separated Index

Inputs

Socket Default Description
Atoms None Atomic geometry that contains vertices and edges
Selection True Selection field for which atoms to separate

Separate Polymers

Separate the input atomic geometry into it’s different polymers or Protein, Nucleic Acid and other.

Outputs

Description Socket
Peptide
Nucleic
Other

Inputs

Socket Default Description
Atoms None Atomic geometry that contains vertices and edges

Select Chain_

Select single or multiple of the different chains. Creates a selection based on the chain_id attribute.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
Chain A True Select the atoms in Chain A
Chain B True Select the atoms in Chain B
Chain ... True Select the atoms in Chain …

Select Entity_

Select single or multiple of the different entities. Creates a selection based on the entity_id attribute.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
Entity A True Select the atoms in Entity A
Entity B True Select the atoms in Entity B
Entity ... True Select the atoms in Entity …

Select Ligand_

Select single or multiple of the different ligands.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
Ligand A True Select the atoms in Ligand A
Ligand B True Select the atoms in Ligand B
Ligand ... True Select the atoms in Ligand …

Select Segment_

Output a selection based on the segment_id that is present in some MD trajectories

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
Segment A True Select the atoms in Ligand A
Segment B True Select the atoms in Ligand B
Segment ... True Select the atoms in Ligand …

Select Atomic Number

Select points based on their atomic_number attribute, corresponding to the element’s atomic number. Useful for selecting single elements quickly

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection
atomic_number 6 Create a selection based on the inputted atomic number.

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

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection
H False Select the element H
He False Select the element He
Li False Select the element Li
Be False Select the element Be
B False Select the element B
C False Select the element C
N False Select the element N
O False Select the element O
F False Select the element F
Ne False Select the element Ne
Na False Select the element Na
Mg False Select the element Mg
Al False Select the element Al
Si False Select the element Si
P False Select the element P
S False Select the element S
Cl False Select the element Cl
Ar False Select the element Ar
K False Select the element K
Ca False Select the element Ca
Sc False Select the element Sc
Ti False Select the element Ti
V False Select the element V
Cr False Select the element Cr
Mn False Select the element Mn
Fe False Select the element Fe
Co False Select the element Co
Ni False Select the element Ni
Cu False Select the element Cu
Zn False Select the element Zn
Ga False Select the element Ga
Ge False Select the element Ge
As False Select the element As
Se False Select the element Se
Br False Select the element Br
Kr False Select the element Kr
Rb False Select the element Rb
Sr False Select the element Sr
Y False Select the element Y
Zr False Select the element Zr
Nb False Select the element Nb
Mo False Select the element Mo
Tc False Select the element Tc
Ru False Select the element Ru
Rh False Select the element Rh
Pd False Select the element Pd
Ag False Select the element Ag
Cd False Select the element Cd
In False Select the element In
Sn False Select the element Sn
Sb False Select the element Sb
Te False Select the element Te
I False Select the element I
Xe False Select the element Xe
Cs False Select the element Cs
Ba False Select the element Ba
La False Select the element La
Ce False Select the element Ce
Pr False Select the element Pr
Nd False Select the element Nd
Pm False Select the element Pm
Sm False Select the element Sm
Eu False Select the element Eu
Gd False Select the element Gd
Tb False Select the element Tb
Dy False Select the element Dy
Ho False Select the element Ho
Er False Select the element Er
Tm False Select the element Tm
Yb False Select the element Yb
Lu False Select the element Lu
Hf False Select the element Hf
Ta False Select the element Ta
W False Select the element W
Re False Select the element Re
Os False Select the element Os
Ir False Select the element Ir
Pt False Select the element Pt
Au False Select the element Au
Hg False Select the element Hg

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

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection
ALA False Select the residue ALA
ARG False Select the residue ARG
ASN False Select the residue ASN
ASP False Select the residue ASP
CYS False Select the residue CYS
GLU False Select the residue GLU
GLN False Select the residue GLN
GLY False Select the residue GLY
HIS False Select the residue HIS
ILE False Select the residue ILE
LEU False Select the residue LEU
LYS False Select the residue LYS
MET False Select the residue MET
PHE False Select the residue PHE
PRO False Select the residue PRO
SER False Select the residue SER
THR False Select the residue THR
TRP False Select the residue TRP
TYR False Select the residue TYR
VAL False Select the residue VAL
A False Select the residue A
C False Select the residue C
G False Select the residue G
T False Select the residue T
rA False Select the residue rA
rC False Select the residue rC
rG False Select the residue rG
rU False Select the residue rU

Select Res ID

Select a atoms based on their res_id number.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection
Res ID 10 A single res_id selection

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.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection
Min 10 Minimum of a res_id range selection
Max 100 Maximum of a res_id range selection

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.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
res_id 10 A single res_id selection
res_id 15 A single res_id selection
res_id: Min 20 Minimum of a res_id range selection
res_id: Max 100 Maximum of a res_id range selection

Select Attribute

Select atoms that have true for the given attribute name.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection
Name is_peptide

Is Peptide

Outputs a selection for all of the points in a peptide

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection

Is Nucleic

Outputs a selection for all of the points in a nucleic acid molecule

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection

Is Lipid

Select the atoms involved in lipid molecules.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection

Is Solvent

Select the atoms that are part of the solvent.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection

Is Alpha Carbon

Outputs a selection for all of the points that are alpha carbons (CA) in the structure

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection

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

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection

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

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection
Include CA True Include the alpha carbon as part of the side chain

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

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection

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

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection

Is Loop

Outputs a selection for those points in a peptide which are not part of any secondary structure (loop or helix)

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection

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.

Outputs

Description Socket
The calculated selection Selection
Expanded Selection that excludes the original selection Bonded

Inputs

Socket Default Description
Selection False Selection of atoms to apply this node to
Depth 1 Number of bonds to expand the selection by

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.

Outputs

Description Socket
The calculated selection Selection

Inputs

Socket Default Description
Selection False Selection of atoms to apply this node to
Expand True Whether to expand the selection to the whole residue if at least one atom is selected

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.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection
Object <bpy_struct, Object(“select_cube”) at 0x13752b220> 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

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.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
And True The resulting selection must overlap with this input selection
Or False The resulting selection can be calculated from this node or be from this input selection
Object <bpy_struct, Object(“select_sphere”) at 0x13752b820> 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

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.

Outputs

Description Socket
The calculated selection Selection
The inverse of the calculated selection Inverted

Inputs

Socket Default Description
Target Atoms None The atoms to measure the distance from.
Subset True Subset of input atoms to use for proximity calculation
Expand False Include an entire residue if even a single atom is within the threshold
Distance (A) 5.0 Cutoff distance for the selection in Angstroms