The question is related to similar issues with standalone package: lots of empty space is added in addition to the desired figure. However, this time no empty paragraphs in source code. My MWE:
\documentclass[convert]{standalone}
\usepackage[english]{babel}
\usepackage{textopo}
\begin{document}
\begin{textopo}
\sequence{EIKKKLFWRAV[VAEFLAMTLFVFISIGSA]LGFNYPLERN}
\end{textopo}
\end{document}
Produces following png after running pdflatex -shell-escape -synctex=1 -interaction=nonstopmode mwe.tex
I suspect that the problem is in textopo package rather than standalone, however, I need confirmation from someone more experienced. And any workaround would be highly appreciated.