--- title: "MoleculePlot3D" language: "en" type: "Symbol" summary: "MoleculePlot3D[mol] creates a three-dimensional model of the molecule mol. MoleculePlot3D[mol, patt] creates a model of mol where all atoms and bonds matching the pattern patt are highlighted." keywords: - 3D - chemistry - chemical structure - Lewis structure - molecular computation - molecular graphics - molecular visualization - molecule - structural depiction - structural diagram - structure diagram canonical_url: "https://reference.wolfram.com/language/ref/MoleculePlot3D.html" source: "Wolfram Language Documentation" related_guides: - title: "Physics & Chemistry: Data and Computation" link: "https://reference.wolfram.com/language/guide/PhysicsAndChemistryDataAndComputation.en.md" - title: "Molecular Structure & Computation" link: "https://reference.wolfram.com/language/guide/MolecularStructureAndComputation.en.md" --- [EXPERIMENTAL] # MoleculePlot3D MoleculePlot3D[mol] creates a three-dimensional model of the molecule mol. MoleculePlot3D[mol, patt] creates a model of mol where all atoms and bonds matching the pattern patt are highlighted. ## Details and Options * If the molecule does not have structure diagram coordinates, they will be generated automatically according to the molecule's ``AtomCoordinates`` option. * ``mol`` can be a ``Molecule`` object or something that can be easily converted to one, such as a systematic chemical name, a ``"Chemical"`` entity or ``ExternalIdentifier``. * Possible forms for ``patt`` include: | | | | ----------------------- | ------------------------------------- | | n | the index of a particular atom | | Atom[…] | a pattern for an atom | | Bond[…] | a pattern for a bond | | MoleculePattern[…] | a pattern for a molecule substructure | | {patt1, patt2, …} | a list of patterns | | <\|label1 -> patt1, …\|> | an Association of labels and patterns | * Patterns entered as ``Style[patt, spec]``will be styled according to ``spec``. * ``MoleculePlot3D`` has the same options as ``Graphics3D``, with the following additions and changes: [] | | | | | ---------------- | --------- | ------------------------------------- | | AtomLabels | None | labels and label placements for atoms | | AtomLabelStyle | Automatic | style to use for atom labels | | BondLabels | None | labels and label placements for bonds | | BondLabelStyle | Automatic | style to use for bond labels | | Boxed | False | whether to draw the bounding box | | ColorRules | Automatic | a list of rules | | IncludeHydrogens | True | whether to show hydrogen atoms | | PlotLegends | None | legends for highlights | | PlotTheme | Automatic | overall theme for the plot | * Supported plot themes include: | | | | | ------- | -------------- | ----------------------------------------------------------------------------- | | [image] | "BallAndStick" | display atoms and bonds using Sphere and Cylinder primitives | | [image] | "Spacefilling" | atoms are depicted with spheres with radius matching the van der Waals radius | | [image] | "Tubes" | atoms omitted | | [image] | "Wireframe" | bonds rendered as lines | * Typical settings for ``PlotLegends`` include: | | | | ---------------- | ---------------------------------- | | None | no legend | | Automatic | automatically determine legend | | {lbl1, lbl2, …} | use lbl1, lbl2, … as legend labels | | Placed[lspec, …] | specify placement for legend | * When ``patt`` is entered as an ``Association``, the ``labeli`` will be used in the ``PlotLegends``. ### List of all options | | | | | -------------------- | --------------- | ---------------------------------------------------------------------------------- | | AlignmentPoint | Center | the default point in the graphic to align with | | AspectRatio | Automatic | ratio of height to width | | AtomLabels | None | labels and label placements for atoms | | AtomLabelStyle | Automatic | style to use for atom labels | | 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 | | BondLabels | None | labels and label placements for bonds | | BondLabelStyle | Automatic | style to use for bond labels | | 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 | a list of rules | | 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 | | IncludeHydrogens | True | whether to show hydrogen atoms | | 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 | legends for highlights | | 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 | | PlotTheme | Automatic | 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 (14) ### Basic Examples (3) Create a molecule and plot it in 3D: ```wl In[1]:= MoleculePlot3D[Molecule["NC(=O)C[C@H](C(=O)O)N"]] Out[1]= [image] ``` Highlight the first and third atoms: ```wl In[2]:= MoleculePlot3D[Molecule["NC(=O)C[C@H](C(=O)O)N"], {1, 3}] Out[2]= [image] ``` Highlight all oxygen atoms: ```wl In[3]:= MoleculePlot3D[Molecule["NC(=O)C[C@H](C(=O)O)N"], Atom["O"]] Out[3]= [image] ``` --- Highlight two different patterns: ```wl In[1]:= MoleculePlot3D["O=C(C1CCC1)S[C@@H]1CCC1(C)C", <|"carbonyl" -> Bond[{"C", "O"}, "Double"], "ring carbons" -> Atom["C", "RingAtomQ" -> True]|>] Out[1]= [image] ``` --- Use different plot themes: ```wl In[1]:= MoleculePlot3D[Molecule["CCCC"], PlotTheme -> #]& /@ {"Wireframe", "Tubes", "BallAndStick", "SpaceFilling"} Out[1]= {[image], [image], [image], [image]} ``` ### Scope (2) A pattern can match one or multiple positions in a molecule: ```wl In[1]:= m = Molecule[{Atom["C"], Atom["C"], Atom["C"], Atom["O"], Atom["N"], Atom["C"], Atom["O"], Atom["N"], Atom["C"], Atom["C"], Atom["C"], Atom["O"], Atom["O"], Atom["C"], Atom["N"], Atom["C"], Atom["C"], Atom["O"], Atom["O"], Atom["C"], Atom["C"], A ... er" -> 10, "Direction" -> "Clockwise", "FiducialAtom" -> 9, "Ligands" -> {11, 5, 34}], Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 16, "Direction" -> "Counterclockwise", "FiducialAtom" -> 15, "Ligands" -> {17, 20, 40}]}]; carbonylPattern = Bond[{"C", "O"}, "Double"]; ``` Highlight each carbonyl separately: ```wl In[2]:= MoleculePlot3D[m, carbonylPattern] Out[2]= [image] ``` Highlight each carbonyl as a single color: ```wl In[3]:= MoleculePlot3D[m, {carbonylPattern}] Out[3]= [image] ``` --- Highlight several patterns: ```wl In[1]:= MoleculePlot3D[Molecule[{Atom["C"], Atom["N"], Atom["C"], Atom["C"], Atom["C"], Atom["N"], Atom["C"], Atom["O"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], A ... e"], Bond[{6, 22}, "Single"], Bond[{10, 23}, "Single"], Bond[{10, 24}, "Single"], Bond[{11, 25}, "Single"], Bond[{11, 26}, "Single"], Bond[{11, 27}, "Single"], Bond[{12, 28}, "Single"], Bond[{12, 29}, "Single"], Bond[{12, 30}, "Single"]}], {1, Bond[{"C", "C"}, "Double"]}] Out[1]= [image] ``` ### Options (8) #### AtomLabels (1) Label all atoms by their index: ```wl In[1]:= MoleculePlot3D[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], AtomLabels -> "AtomIndex"] Out[1]= [image] ``` Label only chlorine atoms by their index: ```wl In[2]:= MoleculePlot3D[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], AtomLabels -> {Atom["Cl"] -> "AtomIndex"}] Out[2]= [image] ``` Label non-hydrogen atoms by their hybridization: ```wl In[3]:= MoleculePlot3D[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], AtomLabels -> {Atom[Except["H"]] -> MoleculeProperty["OrbitalHybridization"]}] Out[3]= [image] ``` #### AtomLabelStyle (1) Set all labels to have the same style: ```wl In[1]:= MoleculePlot3D[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], AtomLabels -> "AtomIndex", AtomLabelStyle -> Directive[FontSize -> 16, Blue]] Out[1]= [image] ``` Set the label style depending on atom type: ```wl In[2]:= MoleculePlot3D[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], AtomLabels -> "AtomIndex", AtomLabelStyle -> {Atom["C"] -> Directive[16, Blue], Atom["O"] -> Directive[22, Purple, Bold], _ -> Italic}] Out[2]= [image] ``` #### BondLabels (1) Label all bonds by their index: ```wl In[1]:= MoleculePlot3D[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], BondLabels -> "BondIndex"] Out[1]= [image] ``` Label only bonds to chlorine atoms by their bond type: ```wl In[2]:= MoleculePlot3D[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], BondLabels -> {Bond[{"Cl", _}] -> MoleculeProperty["BondType"]}] Out[2]= [image] ``` #### BondLabelStyle (1) Give all bond labels the same style: ```wl In[1]:= MoleculePlot3D[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], BondLabels -> "BondIndex", BondLabelStyle -> Directive[FontSize -> 22, Red]] Out[1]= [image] ``` Label bonds differently based on their atoms: ```wl In[2]:= MoleculePlot3D[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], BondLabels -> "BondIndex", BondLabelStyle -> {Bond[{"N", _}] -> Directive[FontSize -> 22, Red], Bond[{"Cl", _}] -> Directive[FontSize -> 22, Blue]}] Out[2]= [image] ``` #### ColorRules (1) Specify different colors for atomic elements: ```wl In[1]:= m = Molecule["Nc1nccc(n1)c1c(C)onc1c1ccccc1"] Out[1]= Molecule[{"N", "C", "N", "C", "C", "C", "N", "C", "C", "C", "O", "N", "C", "C", "C", "C", "C", "C", "C"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Aromatic"], Bond[{3, 4}, "Aromatic"], Bond[{4, 5}, "Aromatic"], Bond[{5, 6}, "Aromatic"], Bond[{6 ... 14}, "Single"], Bond[{14, 15}, "Aromatic"], Bond[{15, 16}, "Aromatic"], Bond[{16, 17}, "Aromatic"], Bond[{17, 18}, "Aromatic"], Bond[{18, 19}, "Aromatic"], Bond[{7, 2}, "Aromatic"], Bond[{13, 8}, "Aromatic"], Bond[{19, 14}, "Aromatic"]}, {}] In[2]:= MoleculePlot3D[m] Out[2]= [image] In[3]:= MoleculePlot3D[m, ColorRules -> {"C" -> RGBColor[0.79, 0.34, 0.5], "N" -> RGBColor[0.5, 0.51, 0.81], _ -> GrayLevel[.7]}] Out[3]= [image] ``` #### IncludeHydrogens (1) By default, all hydrogen atoms are shown: ```wl In[1]:= MoleculePlot3D[Molecule["2-cycloheptanol"]] Out[1]= [image] ``` Show only the heavy atoms: ```wl In[2]:= MoleculePlot3D[Molecule["2-cycloheptanol"], IncludeHydrogens -> None] Out[2]= [image] ``` Create a molecule with only a few explicit hydrogens and show them in 3D: ```wl In[3]:= MoleculePlot3D[Molecule["[H]C([H])=CC"], IncludeHydrogens -> "ExplicitOnly"] Out[3]= [image] ``` #### PlotLegends (1) Use placeholders for plot legends: ```wl In[1]:= m = Molecule[{Atom["C"], Atom["N"], Atom["C"], Atom["C"], Atom["C"], Atom["N"], Atom["C"], Atom["O"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], A ... e"], Bond[{6, 22}, "Single"], Bond[{10, 23}, "Single"], Bond[{10, 24}, "Single"], Bond[{11, 25}, "Single"], Bond[{11, 26}, "Single"], Bond[{11, 27}, "Single"], Bond[{12, 28}, "Single"], Bond[{12, 29}, "Single"], Bond[{12, 30}, "Single"]}]; In[2]:= MoleculePlot3D[m, {1, Bond[{"C", "C"}, "Double"]}, PlotLegends -> Automatic] Out[2]= [image] ``` Use the expressions to label the highlights: ```wl In[3]:= MoleculePlot3D[m, {1, Bond[{"C", "C"}, "Double"]}, PlotLegends -> Placed["Expressions", Below]] Out[3]= [image] ``` #### PlotTheme (1) Use different plot themes to visualize a molecule in 3D: ```wl In[1]:= m = Molecule["Nc1nccc(n1)c1c(C)onc1c1ccccc1"]; In[2]:= MoleculePlot3D[m, PlotTheme -> "Tubes"] Out[2]= [image] In[3]:= MoleculePlot3D[m, PlotTheme -> {"Spacefilling", "Monochrome"}] Out[3]= [image] ``` ### Neat Examples (1) Combine a 3D molecule plot with a surface mesh using ``MoleculeMesh`` : ```wl In[1]:= With[{m = Molecule[{"O", "C", Atom["C", "HydrogenCount" -> 1], "C", "C", "C", Atom["C", "HydrogenCount" -> 1], Atom["C", "HydrogenCount" -> 1], "O", "C", "C", Atom["C", "HydrogenCount" -> 1], Atom["C", "HydrogenCount" -> 1], "C", "O", "C", "O", "N", ... ection" -> "Clockwise"], Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 29, "Direction" -> "Clockwise"], Association["StereoType" -> "DoubleBond", "StereoBond" -> {5, 6}, "Ligands" -> {4, 7}, "Value" -> "Opposite"]}}]}, Show[MoleculePlot3D[m, PlotTheme -> "Tubes"], MoleculeMesh[m, "Gaussian", BaseStyle -> Opacity[0.5]] ] ] Out[1]= [image] ``` ## See Also * [`MoleculePlot`](https://reference.wolfram.com/language/ref/MoleculePlot.en.md) * [`Molecule`](https://reference.wolfram.com/language/ref/Molecule.en.md) * [`AtomLabels`](https://reference.wolfram.com/language/ref/AtomLabels.en.md) * [`AtomLabelStyle`](https://reference.wolfram.com/language/ref/AtomLabelStyle.en.md) * [`BondLabels`](https://reference.wolfram.com/language/ref/BondLabels.en.md) * [`BondLabelStyle`](https://reference.wolfram.com/language/ref/BondLabelStyle.en.md) * [`BioMoleculePlot3D`](https://reference.wolfram.com/language/ref/BioMoleculePlot3D.en.md) * [`MoleculeMesh`](https://reference.wolfram.com/language/ref/MoleculeMesh.en.md) * [`Chemical`](https://reference.wolfram.com/language/ref/entity/Chemical.en.md) * [`Protein`](https://reference.wolfram.com/language/ref/entity/Protein.en.md) * [`MOL`](https://reference.wolfram.com/language/ref/format/MOL.en.md) * [`SDF`](https://reference.wolfram.com/language/ref/format/SDF.en.md) * [`PDB`](https://reference.wolfram.com/language/ref/format/PDB.en.md) ## Related Guides * [Physics & Chemistry: Data and Computation](https://reference.wolfram.com/language/guide/PhysicsAndChemistryDataAndComputation.en.md) * [Molecular Structure & Computation](https://reference.wolfram.com/language/guide/MolecularStructureAndComputation.en.md) ## History * [Introduced in 2019 (12.0)](https://reference.wolfram.com/language/guide/SummaryOfNewFeaturesIn120.en.md) \| [Updated in 2021 (13.0)](https://reference.wolfram.com/language/guide/SummaryOfNewFeaturesIn130.en.md)