Drawing a 3D molecule in TikZ

Question

I'm trying to make a methane molecule in tikz-3d. All that's left is to make the "chemically correct" wedges and dashes. I tried with chemfig, but that only allows for a 2D molecule that pretends to be on 3D. Yet its wedges and dashes are exactly what I want (blue molecule).

I want to use this figure later on, now with 3D vectors and such, so using chemfig is not an option. It has to be a 3D figure. I need some sort of object that looks "triangular-ish" from any angle, so I tried to make cones. My attempt is

\documentclass[tikz]{standalone}
\usetikzlibrary{positioning}
\usepackage{tikz-3dplot,calc}
\usepackage{chemfig}

\begin{document}
\tdplotsetmaincoords{85}{90}% Determines point of view
\begin{tikzpicture}[tdplot_main_coords]

\def\c{1.5}

\coordinate (c01) at (0,0,0);
\coordinate (h01) at (\c,\c,\c);
\coordinate (h02) at (-\c,-\c,\c);
\coordinate (h03) at (\c,-\c,-\c);
\coordinate (h04) at (-\c,\c,-\c);
\coordinate (cor01) at (\c,-\c,\c);
\coordinate (cor02) at (-\c,\c,\c);
\coordinate (cor03) at (\c,\c,-\c);
\coordinate (cor04) at (-\c,-\c,-\c);

% Cube's edges
\begin{scope}[thick,line join = round]
\draw (h01) -- (cor01) -- (h02) -- (cor02) -- cycle;
\draw (h03) -- (cor04) -- (h04) -- (cor03) -- cycle;
\draw (h03) -- (cor01);
\draw (h02) -- (cor04);
\draw (h04) -- (cor02);
\draw (h01) -- (cor03);
\end{scope}

% Attempt to draw a wedge
\coordinate (h01up) at ($(h01)+(-0.2*\c,-0.2*\c,0)$);
\coordinate (h01do) at ($(h01)+(0,0,-0.2*\c)$);
\begin{scope}[very thick]
\draw (c01) -- (h01);
\fill[black] (c01) -- (h01) to [out=0,in=0] (h01do) to [out=180,in=180] (h01up) to [out=0,in=0] (h01do) -- (c01);
\draw[line width=0.25em,dash pattern={on 1pt off 1pt}] (c01) -- (h02);
\draw (c01) -- (h03);
\draw (c01) -- (h04);
\end{scope}

% Atoms
\colorlet{hyd}{white}
\colorlet{carb}{black!80}
\colorlet{atomshell}{black}

\filldraw[fill=carb,draw=atomshell,thick] (c01) circle [radius=10pt];
\filldraw[fill=hyd,draw=atomshell,thick] (h01) circle [radius=5pt];
\filldraw[fill=hyd,draw=atomshell,thick] (h02) circle [radius=5pt];
\filldraw[fill=hyd,draw=atomshell,thick] (h03) circle [radius=5pt];
\filldraw[fill=hyd,draw=atomshell,thick] (h04) circle [radius=5pt];

\node at (h01) [above] {$h_1$};
\node at (h02) [above] {$h_2$};

\begin{scope}[xshift = -7.5em, yshift = -6em]
\draw [->] (0,0,0) -- (0.75,0,0) node [below right=-0.2em and -0.2em] {$x$};
\draw [->] (0,0,0) -- (0,0.75,0) node [below left= -0.2em and -0.2em] {$y$};
\draw [->] (0,0,0) -- (0,0,0.6) node [below left] {$z$};    
\end{scope}

\node at (0,3.5,0) {\color{blue}\chemfig{(-[:215]H)(-[:325]H)(<[:115]H)(<:[:65]H)}};
\end{tikzpicture}
\end{document}

Answer 1

Welcome! Nice question. Here is a way with tangents and clip.

\documentclass[tikz]{standalone}
\usetikzlibrary{backgrounds,positioning}
\usepackage{tikz-3dplot}
\usepackage{chemfig}

\begin{document}
\tdplotsetmaincoords{85}{90}% Determines point of view
\begin{tikzpicture}[tdplot_main_coords,
H atom/.style={circle,fill=hyd,draw=atomshell,thick,inner sep=5pt},
C atom/.style={circle,fill=carb,draw=atomshell,thick,inner sep=10pt}]

\def\c{1.5}

\coordinate (c01) at (0,0,0);

% Cube's edges
\begin{scope}[thick,line join = round]
\draw (\c,\c,\c)  coordinate (h01) 
    -- (\c,-\c,\c) coordinate (cor01) 
    -- (-\c,-\c,\c) coordinate (h02) -- (-\c,\c,\c) coordinate (cor02) 
    -- cycle;
\draw (\c,-\c,-\c) coordinate (h03) edge (cor01)
   -- (-\c,-\c,-\c) coordinate (cor04) edge (cor04) 
    -- (-\c,\c,-\c) coordinate (h04) edge (cor02)
    -- (\c,\c,-\c) coordinate (cor03) edge  (h01) -- cycle;
\end{scope}

% Attempt to draw a wedge
\coordinate (h01up) at ($(h01)+(-0.2*\c,-0.2*\c,0)$);
\coordinate (h01do) at ($(h01)+(0,0,-0.2*\c)$);

% Atoms
\colorlet{hyd}{white}
\colorlet{carb}{black!80}
\colorlet{atomshell}{black}

\path (c01) node[C atom]{}
    foreach \X in {1,...,4}
    {\ifnum\X<3
    (h0\X) node[H atom,label=above:{$h_\X$}](H0\X){}
    \else
    (h0\X) node[H atom](H0\X){}
    \fi   } (h02) edge[thick] (cor01);

\begin{scope}[on background layer]
 \begin{scope}[very thick]
  \draw (c01) -- (H03);
  \draw (c01) -- (H04);
 \end{scope}
 \draw[fill] (tangent cs:node=H01, point={(c01)}, solution=1)
  -- (c01) --  (tangent cs:node=H01, point={(c01)}, solution=2);
 \clip (tangent cs:node=H02, point={(c01)}, solution=1)
  -- (c01) --  (tangent cs:node=H02, point={(c01)}, solution=2);
 \draw[line width=15pt,dash pattern={on 1pt off 1pt}] (c01) -- (h02); 
\end{scope}  
\begin{scope}[xshift = -7.5em, yshift = -6em]
\draw [->] (0,0,0) -- (0.75,0,0) node [below right=-0.2em and -0.2em] {$x$};
\draw [->] (0,0,0) -- (0,0.75,0) node [below left= -0.2em and -0.2em] {$y$};
\draw [->] (0,0,0) -- (0,0,0.6) node [below left] {$z$};    
\end{scope}

\node at (0,3.5,0) {\color{blue}\chemfig{(-[:215]H)(-[:325]H)(<[:115]H)(<:[:65]H)}};
\end{tikzpicture}
\end{document}

If you do not want to clip, you can use the expanding waves decoration.

\documentclass[tikz]{standalone}
\usetikzlibrary{backgrounds,positioning,decorations.pathreplacing}
\usepackage{tikz-3dplot}
\usepackage{chemfig}

\begin{document}
\tdplotsetmaincoords{85}{90}% Determines point of view
\begin{tikzpicture}[tdplot_main_coords,
H atom/.style={circle,fill=hyd,draw=atomshell,thick,inner sep=5pt},
C atom/.style={circle,fill=carb,draw=atomshell,thick,inner sep=10pt}]

\def\c{1.5}

\coordinate (c01) at (0,0,0);

% Cube's edges
\begin{scope}[thick,line join = round]
\draw (\c,\c,\c)  coordinate (h01) 
    -- (\c,-\c,\c) coordinate (cor01) 
    -- (-\c,-\c,\c) coordinate (h02) -- (-\c,\c,\c) coordinate (cor02) 
    -- cycle;
\draw (\c,-\c,-\c) coordinate (h03) edge (cor01)
   -- (-\c,-\c,-\c) coordinate (cor04) edge (cor04) 
    -- (-\c,\c,-\c) coordinate (h04) edge (cor02)
    -- (\c,\c,-\c) coordinate (cor03) edge  (h01) -- cycle;
\end{scope}

% Attempt to draw a wedge
\coordinate (h01up) at ($(h01)+(-0.2*\c,-0.2*\c,0)$);
\coordinate (h01do) at ($(h01)+(0,0,-0.2*\c)$);

% Atoms
\colorlet{hyd}{white}
\colorlet{carb}{black!80}
\colorlet{atomshell}{black}

\path (c01) node[C atom]{}
    foreach \X in {1,...,4}
    {\ifnum\X<3
    (h0\X) node[H atom,label=above:{$h_\X$}](H0\X){}
    \else
    (h0\X) node[H atom](H0\X){}
    \fi   } (h02) edge[thick] (cor01);

\begin{scope}[on background layer]
 \begin{scope}[very thick]
  \draw (c01) -- (H03);
  \draw (c01) -- (H04);
 \end{scope}
 \draw[fill] (tangent cs:node=H01, point={(c01)}, solution=1)
  -- (c01) --  (tangent cs:node=H01, point={(c01)}, solution=2);
 \draw[decorate,decoration={expanding waves,angle=5,segment length=3pt},very thick]   
 (c01) -- (h02);  
\end{scope}
\begin{scope}[xshift = -7.5em, yshift = -6em]
\draw [->] (0,0,0) -- (0.75,0,0) node [below right=-0.2em and -0.2em] {$x$};
\draw [->] (0,0,0) -- (0,0.75,0) node [below left= -0.2em and -0.2em] {$y$};
\draw [->] (0,0,0) -- (0,0,0.6) node [below left] {$z$};    
\end{scope}
\node at (0,3.5,0) {\color{blue}\chemfig{(-[:215]H)(-[:325]H)(<[:115]H)(<:[:65]H)}};
\end{tikzpicture}
\end{document}

Addendum: just for fun. This requires the 3d tools library. This achieves 3d ordering in a convention-independent way. As long as you have some means that provides you with an oriented orthographic projection of the coordinates, the function screendepth will provide you with the 3d distance from the virtual screen. Coordinates that are closer to the viewer will have a larger screen depth. Tools that achieve orthographic projections include are tikz-3dplot and the perspective library, but their conventions differ. The function here uses the TikZ coordinates. In particular, this also means that we can fully reconstruct the rotation matrix just from TikZ' book keeping variables like \pgf@xx. The following animation shows a possible application. If the bond goes to an object that is further away, it is dashed, if the atoms is closer, it is a wedge and if the atoms are roughly equally far away just at thick line. I payed zero attention to the cube lines.

\documentclass[tikz]{standalone}
\usetikzlibrary{backgrounds,positioning,decorations.pathreplacing,fpu,3dtools}
\usepackage{tikz-3dplot}
\usepackage{chemfig}
\makeatletter
\pgfmathdeclarefunction{screendepth}{1}{%
\begingroup%
\edef\mycoord{\RawCoord(#1)}%
\edef\screenvec{{(\the\pgf@yx)*(\the\pgf@zy)-(\the\pgf@yy)*(\the\pgf@zx)},%
{(\the\pgf@zx)*(\the\pgf@xy)-(\the\pgf@xx)*(\the\pgf@zy)},%
{(\the\pgf@xx)*(\the\pgf@yy)-(\the\pgf@yx)*(\the\pgf@xy)}}%
\pgfkeys{/pgf/fpu,/pgf/fpu/output format=fixed}%
\pgfmathparse{TD("(#1)o(\screenvec)")/1cm/1cm}%
\pgfmathsmuggle\pgfmathresult\endgroup%
}%

\makeatother
\newcommand\ConnectAtoms[3][]{%
\pgfmathsetmacro{\depthA}{screendepth("#2")}%
\pgfmathsetmacro{\depthB}{screendepth("#3")}%
\pgfmathtruncatemacro{\itest}{1+(abs(\depthA-\depthB)<0.1 ?0 : sign(\depthA-\depthB))}%
\ifcase\itest
\draw[decorate,decoration={expanding waves,angle=5,segment length=3pt},
 very thick,#1]   
 (#2) -- (#3);
\or
\draw[very thick,#1]   
 (#2) -- (#3);
\or
\path[fill,#1] (tangent cs:node=#3, point={(#2)}, solution=1)
  -- (#2) --  (tangent cs:node=#3, point={(#2)}, solution=2);
\fi
}


\begin{document}
\foreach \Angle in {5,15,...,355}
{\tdplotsetmaincoords{90+20*cos(\Angle)}{\Angle}% Determines point of view
\begin{tikzpicture}[tdplot_main_coords,
H atom/.style={circle,fill=hyd,draw=atomshell,thick,inner sep=5pt},
C atom/.style={circle,fill=carb,draw=atomshell,thick,inner sep=10pt}]
% Atoms
\colorlet{hyd}{white}
\colorlet{carb}{black!80}
\colorlet{atomshell}{black}
\path[tdplot_screen_coords,use as bounding box] (-3,-3) rectangle (3,3);
\def\c{1.5}

\path  (0,0,0) coordinate  (c01) node[C atom]{};

% Cube's edges
\begin{scope}[thick,line join = round]
\draw (\c,\c,\c)  coordinate (h01) node[H atom,label=above:{$h_1$}](H01){}
    -- (\c,-\c,\c) coordinate (cor01) 
    -- (-\c,-\c,\c) coordinate (h02) node[H atom,label=above:{$h_2$}](H02){}
    -- (-\c,\c,\c) coordinate (cor02) 
    -- cycle;
\draw (\c,-\c,-\c) coordinate (h03) node[H atom](H03){}  
   -- (-\c,-\c,-\c) coordinate (cor04) edge (H02) 
    -- (-\c,\c,-\c) coordinate (h04) node[H atom](H04){} 
    -- (\c,\c,-\c) coordinate (cor03) edge  (H01) -- cycle
    (cor01) edge (H03) 
    (cor02) edge (H04);
\end{scope}



\path (h02) edge[thick] (cor01)
    (h04) edge[thick] (cor03);
\pgfmathsetmacro{\depthA}{screendepth("c01")}%  
\pgfmathsetmacro{\depthB}{screendepth("h03")}%
\begin{scope}[on background layer]
 \foreach \X in {1,2,3,4}
 {\ConnectAtoms{c01}{H0\X}}
\end{scope}
\end{tikzpicture}}
\end{document}