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Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...he same protein. All \ca /- and \cb /-atoms are shown as spher... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...orange. The convex hull for the \ca /- and \cb /-atomic coordi... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ... convex hull for the \ca /- and \cb /-atomic coordinates is sh... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...e peripheral proteins (\periphcolor /) and the reference set (... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ... /) and the reference set (\tmcolor /). The horizontal axes sh... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...sion, measured as the number of \ca / and \cb / atoms within $... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...ured as the number of \ca / and \cb / atoms within $1 nm$. Ver... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...isely, the vertical axis shows $\OR {A, B,\hat {F}_{\mathrm {h... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ... protein density defined in~\matmet /. Error bars are 95\% con... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...isely, we show the comparisons $\OR {set,null,\hat {F}^{\mathr... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...f peripheral proteins (\periphcolor /) and the reference set (... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ... /) and the reference set (\tmcolor /), and $null$ represent t... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...protrusions as described in~\matmet /. Error bars are 95\% con... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...e peripheral proteins (\periphcolor /) and the reference set (... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ... /) and the reference set (\tmcolor /). We have differentiated... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...he convex hull (in blue) of the \ca / and \cb /-atoms of selec... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...hull (in blue) of the \ca / and \cb /-atoms of selected periph... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...l membrane binding domains. The \cb /-atoms of \emph {the Like... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...are shown as orange spheres and \cb /-atoms of experimentally ... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...s marked with a cross at 180\degree . This is 1f6s which is an... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...in each family (measured at the \ca /-atom). Values greater th... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...$, and panel B the comparisons $\OR {A,B, \hat {F}_{\mathrm {h... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...m peripheral proteins (\periphcolor /) and from proteins in th... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...eins in the reference set (\tmcolor /). In panel B, the contra... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. ./protrusion_ms_suppmat.tex:7: Undefined control sequence. ...y the vertical axis denote $\ln \OR {\mathrm {peripheral}, \ma... l.7 \externalcitedocument {protrusion_ms} The control sequence at the end of the top line of your error message was never \def'ed. If you have misspelled it (e.g., `\hobx'), type `I' and the correct spelling (e.g., `I\hbox'). Otherwise just continue, and I'll forget about whatever was undefined. Package xc Info: IMPORTING LABELS FROM protrusion_ms.aux on input line 7. (/opt/local/share/texmf-texlive/tex/latex/graphics/color.sty Package: color 2014/10/28 v1.1a Standard LaTeX Color (DPC) (/opt/local/share/texmf-texlive/tex/latex/latexconfig/color.cfg File: color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive ) Package color Info: Driver file: pdftex.def on input line 142. 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