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I have a small alignment/spacing issue with a chemical figure. I'm using this -X> arrow that I stumbled across in this post I believe. But as you can see with the debug information on, the structure of glycine is overlaying with that of glutamylcysteine. On top of that the distance between the structure and the "Glycin" label is bigger than the distance to the label/chemname of the other structures. I don't know how I can fix this without making the -X> arrow weirdly long. Can anyone help?

enter image description here

My code (excuse the long preamble, it's for the -X> arrow; refer to the post linked above):

\documentclass{scrbook}
\usepackage[utf8]{inputenc}
\usepackage{chemfig,chemformula}
\usepackage[version=4,arrows=pgf-filled]{mhchem}
\usepackage{tikz-cd}
\usetikzlibrary{shapes.geometric, arrows}
\usepackage{amsmath,amssymb}

% allow for editing Chemfig 
\catcode`\_=11
 
% Initial arguments:
% #1, #2: Same as for -U> (above arrow)
% #3: Additional label at midpoint (also above arrow)
% #4, #5, #6: Like #1, #2, and #3, but below arrow
% #7: Optional shift, default 0
% #8: Optional arrow radius
% #9: Optional arrow angle   
\definearrow9{-X>}{%
    \CF_arrowshiftnodes{#7}%
    \expandafter\draw\expandafter[\CF_arrowcurrentstyle](\CF_arrowstartnode)--(\CF_arrowendnode)node[midway](Xarrowarctangent){};%
    \CF_ifempty{#8}
        {\def\CF_Xarrowradius{0.333}}
        {\def\CF_Xarrowradius{#8}}%
    \CF_ifempty{#9}%
        {\def\CF_Xarrowabsangle{60}}
        {\pgfmathsetmacro\CF_Xarrowabsangle{abs(#9)}}
    % Draw top arrow (start)
    \edef\CF_tmpstr{[\CF_ifempty{#1}{draw=none}{\unexpanded\expandafter{\CF_arrowcurrentstyle}},-]}%
    \expandafter\draw\CF_tmpstr (Xarrowarctangent)%
    arc[radius=\CF_compoundsep*\CF_currentarrowlength*\CF_Xarrowradius,start angle=\CF_arrowcurrentangle-90,delta angle=-\CF_Xarrowabsangle]node(Xarrow1start){};
    % Draw bottom arrow (end)
    \edef\CF_tmpstr{[\CF_ifempty{#2}{draw=none}{\unexpanded\expandafter{\CF_arrowcurrentstyle}},-CF]}%
    \expandafter\draw\CF_tmpstr (Xarrowarctangent)%
    arc[radius=\CF_compoundsep*\CF_currentarrowlength*\CF_Xarrowradius,%
    start angle=\CF_arrowcurrentangle-90,%
    delta angle=\CF_Xarrowabsangle]%
    node(Xarrow1end){};
    % Draw bottom arrow (start)
    \edef\CF_tmpstr{[\CF_ifempty{#4}{draw=none}{\unexpanded\expandafter{\CF_arrowcurrentstyle}},-]}%
    \expandafter\draw\CF_tmpstr (Xarrowarctangent)%
    arc[radius=\CF_compoundsep*\CF_currentarrowlength*\CF_Xarrowradius,start angle=\CF_arrowcurrentangle+90,delta angle=\CF_Xarrowabsangle]node(Xarrow2start){};
    % Draw bottom arrow (end)
    \edef\CF_tmpstr{[\CF_ifempty{#5}{draw=none}{\unexpanded\expandafter{\CF_arrowcurrentstyle}},-CF]}%
    \expandafter\draw\CF_tmpstr (Xarrowarctangent)%
    arc[radius=\CF_compoundsep*\CF_currentarrowlength*\CF_Xarrowradius,%
    start angle=\CF_arrowcurrentangle+90,%
    delta angle=-\CF_Xarrowabsangle]%
    node(Xarrow2end){};
    % Insert labels
    \pgfmathsetmacro\CF_tmpstra{\CF_Xarrowradius*cos(\CF_arrowcurrentangle)<0?"-":"+"}%
    \pgfmathsetmacro\CF_tmpstrb{\CF_Xarrowradius*cos(\CF_arrowcurrentangle)<0?"+":"-"}%
    \ifdim\CF_Xarrowradius pt>0 pt
        \CF_arrowdisplaylabel{#1}{0}\CF_tmpstra{Xarrow1start}{#2}{1}\CF_tmpstra{Xarrow1end}%
        \CF_arrowdisplaylabel{#4}{0}\CF_tmpstrb{Xarrow2start}{#5}{1}\CF_tmpstrb{Xarrow2end}%
        \CF_arrowdisplaylabel{#3}{0.5}\CF_tmpstra\CF_arrowstartnode{}{}{}\CF_arrowendnode%
        \CF_arrowdisplaylabel{#6}{0.5}\CF_tmpstrb\CF_arrowstartnode{}{}{}\CF_arrowendnode%
    \else
        \CF_arrowdisplaylabel{#2}{0}\CF_tmpstra{Xarrow1start}{#1}{1}\CF_tmpstra{Xarrow1end}%
        \CF_arrowdisplaylabel{#5}{0}\CF_tmpstrb{Xarrow2start}{#4}{1}\CF_tmpstrb{Xarrow2end}%
        \CF_arrowdisplaylabel{#3}{0.5}\CF_tmpstra\CF_arrowstartnode{}{}{}\CF_arrowendnode%
        \CF_arrowdisplaylabel{#6}{0.5}\CF_tmpstrb\CF_arrowstartnode{}{}{}\CF_arrowendnode%
    \fi
}
% stop editting chemfig
\catcode`\_=8

\begin{document}

\begin{figure}
\centering
\setchemfig{scheme debug=true}
\schemestart
    \chemname{\chemfig{(-[:145,0.75]HOOC)(-[:270,0.75]NH_2)(-[:35,0.75]-[:325,0.75]-[:35,0.75](=[:90,0.75]O)-[:325,0.75]OH)}}{\color{blue!70}Glutamat}
    \+
    \chemname{\chemfig{(-[:145,0.75]HOOC)(-[:270,0.75]NH_2)(-[:35,0.75]-[:325,0.75]SH)}}{\color{blue!70}Cystein}
    \arrow(@c1.293--){-X>[*{0.180}\small\chemfig{ATP}][*{0.180}\small\chemfig{ADP+P_i}][][][][*{0}\small \color{blue!70}Glutamyl-Cystein-Ligase][][]}[-90,1]
    \chemname{\chemfig{(-[:145,0.75]HOOC)(-[:270,0.75]NH_2)(-[:35,0.75]-[:325,0.75]-[:35,0.75](=[:90,0.75]O)-[:325,0.75]\chembelow{N}{H}-[:35,0.75](-[:90,0.75]-[:135,0.75]HS)-[:325,0.75]COOH)}}{\color{blue!70}$\gamma$-Glutamylcystein}
    \arrow(@c2--){-X>[*{0.180}\small\chemfig{ATP}][*{0.180}\small\chemfig{ADP+P_i}][*{0}\small \color{blue!70}Glutathion-Synthetase][*{0}\chemname{\chemfig{NH_2-[:90,0.75]-[:35,0.75](=[:90,0.75]O)(-[:325,0.75]OH)}}{\color{blue!70}Glycin}][][][][]}[-90,2]
    \chemname{\chemfig{(-[:145,0.75]HOOC)(<:[:270,0.75]NH_2)(-[:35,0.75]-[:325,0.75]-[:35,0.75](=[:90,0.75]O)-[:325,0.75]\chembelow{N}{H}>[:35,0.75](-[:90,0.75]-[:135,0.75]HS)-[:325,0.75](=[:270,0.75]O)-[:35,0.75]\chemabove{N}{H}-[:325,0.75,1]-[:35,0.75]COOH)}}{\color{blue!70}Glutathion}
\schemestop
\end{figure}
\end{document}
2

a little change on the arrow

\arrow(@c2--){-X>[*{0.180}\small\chemfig{ATP}][*{0.180}\small\chemfig{ADP+P_i}][*{0}\small \color{blue!70}Glutathion-Synthetase][*{0.45}\chemname{\chemfig{NH_2-[:90,0.75]-[:35,0.75](=[:90,0.75]O)(-[:325,0.75]OH)}}{\color{blue!70}Glycin}][][][][0.25]}[-90,3]

enter image description here

Update: A complete solution

\schemestart
\subscheme{\chemname{\chemfig{NH_2-[2,0.75,1](-[:145,0.75]HOOC)-[:35,0.75]-[:325,0.75]-[:35,0.75](-[:325,0.75]OH)=[:90,0.75]O}}{\color{blue!70}Glutamat}
\arrow{0}[,0.2] \+ \arrow{0}[,0.2]
\chemname{\chemfig{NH_2-[2,0.75,1](-[:145,0.75]HOOC)-[:35,0.75](=[:90,0.75,,,draw=none]\phantom{O})-[:325,0.75]SH}}{\color{blue!70}Cystein}}
\arrow(@c1.295--){-X>[*{0.180}\small\chemfig{ATP}][*{0.180}\small\chemfig{ADP+P_i}][][][][*{0}\small \color{blue!70}Glutamyl-Cystein-Ligase][][]}[-90,1]
\chemname{\chemfig{NH_2-[2,0.75,1](-[:145,0.75]HOOC)-[:35,0.75]-[:325,0.75]-[:35,0.75](=[:90,0.75]O)-[:325,0.75]\chembelow{N}{H}-[:35,0.75](-[:90,0.75]-[:135,0.75]HS)-[:325,0.75]COOH}}{\color{blue!70}$\gamma$-Glutamylcystein}
\arrow{-X>[*{0.180}\small\chemfig{ATP}][*{0.180}\small\chemfig{ADP+P_i}][*{0}\small\color{blue!70}Glutathion-Synthetase][*{0.45}\chemname{\chemfig{NH_2-[2,0.75]-[:35,0.75](-[:-35,0.75]OH)=[2,0.75]O}}{\color{blue!70}Glycin}][][][][0.25]}[-90,2.6]
\chemname{\chemfig{(-[:145,0.75]HOOC)(<:[:270,0.75]NH_2)(-[:35,0.75]-[:325,0.75]-[:35,0.75](=[:90,0.75]O)-[:325,0.75]\chembelow{N}{H}>[:35,0.75](-[:90,0.75]-[:135,0.75]HS)-[:325,0.75](=[:270,0.75]O)-[:35,0.75]\chemabove{N}{H}-[:325,0.75,1]-[:35,0.75]COOH)}}{\color{blue!70}Glutathion}
\schemestop

enter image description here

1
  • Thank you so much! Especially for perfectly aligning the first arrow with the plus sign, which was like 2 pixels off before, so good work on that!
    – Lilo
    May 24 at 13:34

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