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tl dr; Putting it all together Little background first Anki uses latex compiler to create .dvi intermediate documents from the input LaTeX code, which are then converted to .png bitmap image using dvipng converter. Anki is only able to work with .png picture format! Now, TikZ is (in vast majority of cases) only able to be compiled with pdflatex compiler, ...

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It's a problem due to how the conversion works. The file is actually compiled twice, but one time essentially without any package and so when the aux file is read in this phase, the command is not defined. Workaround: \providecommand{\pgfsyspdfmark}[3]{} \documentclass[convert={convertexe={convert}}]{standalone} \usepackage[utf8]{inputenc} \usepackage{...

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As I'm sure you know when you have used chemfig already the bonds have optional arguments. The manual says: 6 Customization of bonds There is a fifth and last optional argument for bonds which is found after the fourth comma: [,,,,<tikz code>] This means all you have to do is adding the TikZ code for not-drawing: \chemfig{-C-[,,,,draw=...

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