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 Nucleic Type

Select either purines or pyrimidines

Outputs

Description	Socket
	is_purine
	is_pyrimidine

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 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 Hydrogen

Outputs a selection for all of the hydrogen atoms in the structure

Outputs

Description	Socket
Computed selection that includes Hydrogen atoms	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 0x11b078c20>	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 0x11b079220>	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