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I nearly finished one Figure for my thesis, but there are still some issues and with some I do not understand what I am doing wrong:

  1. I wanted to draw a arrow pointing from the red CH3 molecule of SAM to the NH of g molecule. As you can see I could point the arrow to NH but not starting from CH3.

EDIT: Atom style instead of scale box solved the problem.

  1. Is there a way to leave a little space between the blue arrow and the N and CH3 atom?

EDIT: Solved with \draw[shorten <=4pt,shorten >=4pt]

  1. Is it possible to increasse the lenght of the bottom arrow of the reaction without shifting the picture? Or can I just reduce the lenght of the upper arrow an put some space between the 2 molecules?

  2. [optional] I do not know if I am too happy that the names of SAM and SAH are not below the molecule. LaTex does this by itself for some reason.

  3. [optional] When I print it out the smaller molecules are not easy to read. Is there a possibility to give it more contrast? (But maybe it is just a bad printer)

I would appreciate any suggestions.Thanks

Output: enter image description here

0

1 Answer 1

1

for the third question

\arrow{-U>[{\chemfig[atom style={scale=0.5}]{!{sam}}}{SAM}][{\chemfig[atom style={scale=0.5}]{!{sah}}}{SAH}][][0.4][60]}[,4]

enter image description here

Update

\documentclass{article}
\usepackage[showframe]{geometry}
\usepackage{chemfig}
\usepackage{lipsum}

\begin{document}
    

\definesubmol{ch3}{{\color{red}C}|{\color{red}H_3}}
%\chemfig{!{ch3}} %draws red CH3 molecule of SAM

\definesubmol{sam}{*6(=N-*5(-N(>*5(-O-([-3]<-[3]S\rlap{${}^+$}(-[2,,1]@{c}!{ch3})-[-3]-[3]-[-3]C([-2]<NH_2)-[3]([2]=O)-[-3]{\llap{${}^-$}O})-(<:OH)-(<:OH)-))-=N-)=-(-NH_2)=N-)}
%\chemfig{!{sam}} %draws SAM molecule

\definesubmol{sah}{*6(=N-*5(-N(>*5(-O-([-3]<-[3]S-[-3]-[3]-[-3]C([-2]<NH_3\rlap{${}^+$})-[3]([2]=O)-[-3]{\llap{${}^-$}O})-(<:OH)-(<:OH)-))-=N-)=-(-NH_2)=N-)}
%\chemfig{!{sah}} %draws SAH molecule

\definesubmol{g}{H_{2}N-[:30]*6(=N-*5(-N(>*5(-O-(<-[4]O-[4]P(-[2]O\rlap{${}^-$})(-[4,1]{\llap{${}^-$}O})=[-2]O)-(<:O-[:0,0.8])-(<:OH)-))-=N-)=-(=O)-H@{n}N-[,,2])}
%\chemfig{!{g}} %draws g molecule

\definesubmol{m1g}{H_{2}N-[:30]*6(=N-*5(-N(>*5(-O-(<-[4]O-[4]P(-[2]O\rlap{${}^-$})(-[4,1]{\llap{${}^-$}O})=[-2]O)-(<:O-[:0,0.8])-(<:OH)-))-=N-)=-(=O)-N(-{\color{red}H_3}|{\color{red}C})-)}
%\chemfig{!{m1G}} %draws m1G molecule
   
   
\lipsum[2]

\begin{figure}[h]
    \centering
    \scalebox{0.6}{
        \schemestart[0,2.5]
        \chemname{\chemfig[atom style={scale=0.8}]{!{g}}}{guanosine$^{9}$ in tRNA}
        \hspace{1.5cm}
        \arrow{-U>[{\chemfig[atom style={scale=0.5}]{!{sam}}}{SAM}][{\chemfig[atom style={scale=0.5}]{!{sah}}}{SAH}][][0.6][60]}
        \chemmove[blue,dash pattern = on 2pt off 1pt]{\draw(c.120)..  controls +(125:0.5cm) and +(90:4cm)..  (n.90);}
        \hspace{2cm}
        \chemname{\chemfig[atom style={scale=0.8}]{!{m1g}}}{N$^{1}$-methylguanosine in tRNA}
        \schemestop\bigskip
    }
    \chemnameinit{}
    \caption{tRNA methylation:\lipsum[1]} \label{fig:tRNA methylation}  
\end{figure}

\clearpage

\lipsum[2]

\begin{figure}[h]
    \centering
    \scalebox{0.6}{
        \schemestart[0,2.5]
        \chemname{\chemfig[atom style={scale=0.8}]{!{g}}}{guanosine$^{9}$ in tRNA}
        \hspace{0.15cm}
        \arrow{-U>[{\chemfig[atom style={scale=0.5}]{!{sam}}}{SAM}][{\chemfig[atom style={scale=0.5}]{!{sah}}}{SAH}][][0.37][60]}[,4]
        \chemmove[blue,dash pattern = on 2pt off 1pt]{\draw(c.120)..  controls +(125:0.5cm) and +(90:4cm)..  (n.90);}
        \hspace{0.65cm}
        \chemname{\chemfig[atom style={scale=0.8}]{!{m1g}}}{N$^{1}$-methylguanosine in tRNA}
        \schemestop\bigskip
    }
    \chemnameinit{}
    \caption{tRNA methylation:\lipsum[1]} \label{fig:tRNA methylation2}  
\end{figure}
\end{document}

enter image description here

2
  • 1
    thanks. But it also shifts the whole figure to the right and it is no longer centered.
    – Roland
    Commented Oct 28, 2020 at 10:28
  • 1
    You may need to adjust the \hspace and the fourth optional argument of the arrow. See update.
    – polyn
    Commented Oct 28, 2020 at 13:20

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