BioMoleculePlot3D

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`BioMoleculePlot3D`

New in 14.1[Experimental]

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BioMoleculePlot3D[biomol]

creates a three-dimensional graphic of the biomolecule biomol.

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BioMoleculePlot3D[biomolpart]

shows only the part part of biomol.

Details and Options

BioMoleculePlot3D returns a Graphics3D expression.
biomol can be a BioMolecule object or an object that can straightforwardly be converted into one, such as an ExternalIdentifier, peptide BioSequence or "Protein" Entity.
For inputs of the form BioMoleculePlot3D[biomolpart], part should be an Association whose keys and default values are given by:
"ModelNumber" 1 which model to use

"Chains" All which chains to include
Some biomolecules contain information about biological assemblies, which feature various combinations of the chains, along with geometric transformations. Use BioMoleculePlot3D[biomol<|"AssemblyNumber"n|>] to efficiently plot biological assembly number n.
BioMoleculePlot3D has the same options as Graphics3D, with the following additions and changes: [List of all options]

Boxed	False	whether to draw the bounding box
ColorRules	Automatic	rules for coloring of chains
IncludeWaters	False	whether to show disconnected water molecules
PlotLegends	None	legend for chain coloring
PlotStyle	Automatic	an overall style for all chains
PlotTheme	$PlotTheme	overall theme for the plot

Polymeric chains such as polypeptides, DNA and RNA are displayed using a cartoon representation showing the polymer backbone as a tube and various secondary structures such as helices, sheets and nucleic acid rings.
Disconnected components of the biomol that are not part of a polymer chain, known as ligands, are shown as they would be by MoleculePlot3D.
Typical settings for ColorRules include:

	Automatic	color chains automatically
	{"a_i"col_i,…}	color the chain with label a_i with col_i
	{"Residues","res_i"col_i,…}	color by residue name
	{{"a_i",j}col_ij,…}	color the residue with index j on the chain with label a_i with col_i

For a list of chain labels of biomol, use BioMoleculeValue[biomol,"PolymerChainLabels"].
For a list of residue names of biomol use BioMoleculeValue[biomol,"ResidueNames"].
Supported plot themes include:

		"Ribbons"	display polymer chains as ribbons
		"Backbone"	display polymer chains as ribbons
		"SolventAccessibleSurface"	solvent accessible surface
		"GaussianSurface"	Gaussian surface
		"VanDerWaalsSurface"	van der Waals surface
		"BallAndStick"	display atoms and bonds using Sphere and Cylinder primitives
		"Tubes"	display bonds as tubes with no atoms
		"Spacefilling"	atoms are depicted with spheres with radius matching the van der Waals radius

Typical settings for PlotLegends include:
None no legend

Automatic automatically determine legend

Placed[lspec,…] specify placement for legend

List of all options

AlignmentPoint	Center	the default point in the graphic to align with
AspectRatio	Automatic	ratio of height to width
Axes	False	whether to draw axes
AxesEdge	Automatic	on which edges to put axes
AxesLabel	None	axes labels
AxesOrigin	Automatic	where axes should cross
AxesStyle	{}	graphics directives to specify the style for axes
Background	None	background color for the plot
BaselinePosition	Automatic	how to align with a surrounding text baseline
BaseStyle	{}	base style specifications for the graphic
Boxed	False	whether to draw the bounding box
BoxRatios	Automatic	bounding 3D box ratios
BoxStyle	{}	style specifications for the box
ClipPlanes	None	clipping planes
ClipPlanesStyle	Automatic	style specifications for clipping planes
ColorRules	Automatic	rules for coloring of chains
ContentSelectable	Automatic	whether to allow contents to be selected
ControllerLinking	False	when to link to external rotation controllers
ControllerPath	Automatic	what external controllers to try to use
Epilog	{}	2D graphics primitives to be rendered after the main plot
FaceGrids	None	grid lines to draw on the bounding box
FaceGridsStyle	{}	style specifications for face grids
FormatType	TraditionalForm	default format type for text
ImageMargins	0.	the margins to leave around the graphic
ImagePadding	All	what extra padding to allow for labels, etc.
ImageSize	Automatic	absolute size at which to render the graphic
IncludeWaters	False	whether to show disconnected water molecules
LabelStyle	{}	style specifications for labels
Lighting	Automatic	simulated light sources to use
Method	Automatic	details of 3D graphics methods to use
PlotLabel	None	a label for the plot
PlotLegends	None	legend for chain coloring
PlotRange	All	range of values to include
PlotRangePadding	Automatic	how much to pad the range of values
PlotRegion	Automatic	final display region to be filled
PlotStyle	Automatic	an overall style for all chains
PlotTheme	$PlotTheme	overall theme for the plot
PreserveImageOptions	Automatic	whether to preserve image options when displaying new versions of the same graphic
Prolog	{}	2D graphics primitives to be rendered before the main plot
RotationAction	"Fit"	how to render after interactive rotation
SphericalRegion	Automatic	whether to make the circumscribing sphere fit in the final display area
Ticks	Automatic	specification for ticks
TicksStyle	{}	style specification for ticks
TouchscreenAutoZoom	False	whether to zoom to fullscreen when activated on a touchscreen
ViewAngle	Automatic	angle of the field of view
ViewCenter	Automatic	point to display at the center
ViewMatrix	Automatic	explicit transformation matrix
ViewPoint	{1.3,-2.4,2.}	viewing position
ViewProjection	Automatic	projection method for rendering objects distant from the viewer
ViewRange	All	range of viewing distances to include
ViewVector	Automatic	position and direction of a simulated camera
ViewVertical	{0,0,1}	direction to make vertical

Examples

open allclose all

Basic Examples (2)Summary of the most common use cases

Create a biomolecule from an ExternalIdentifier:

In[1]:=1

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https://wolfram.com/xid/0gcv2g48xrwr9036wo-c0iao7

Out[1]=1

In[2]:=2

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https://wolfram.com/xid/0gcv2g48xrwr9036wo-5tyj6q

Out[2]=2

Plot just the first chain:

In[3]:=3

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https://wolfram.com/xid/0gcv2g48xrwr9036wo-yy6h3r

In[4]:=4

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https://wolfram.com/xid/0gcv2g48xrwr9036wo-s3wl5k

View a biomolecule using a Gaussian surface representation:

In[1]:=1

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https://wolfram.com/xid/0gcv2g48xrwr9036wo-s96g5y

Out[1]=1

Scope (1)Survey of the scope of standard use cases

Show the ribbon diagram for an alpha helix along with an all-atom representation:

In[1]:=1

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https://wolfram.com/xid/0gcv2g48xrwr9036wo-22gul9

Out[1]=1

Options (5)Common values & functionality for each option

ColorRules (3)

Use ColorRules to control the styling of polymer chains. This example provides explicit colors for four chains and a default color for all other chains:

In[1]:=1