%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% %%%%% Default parameter settings for the LaTeX ``TeXtopo'' package %%%%% %%%%% %%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% %%%%% This example file contains all standard settings of the TeXtopo %%%%% %%%%% package. It can be used as a template for the creation of perso- %%%%% %%%%% nal parameter files. All TeXtopo user commands are allowed and %%%%% %%%%% functional when specified here. %%%%% %%%%% %%%%% %%%%% To activate these settings for your topology plot load this file %%%%% %%%%% by naming it as optional parameter at the beginning of the tex- %%%%% %%%%% topo environment, e.g. %%%%% %%%%% %%%%% %%%%% \begin{textopo}[myparameterfile] %%%%% %%%%% . %%%%% %%%%% . %%%%% %%%%% \end{textopo} %%%%% %%%%% %%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \Nterm{intra} % Assume N-terminus intracellular \loopextent{30} % Set loop extent to 30 residues \shadingcolors{blues} % Use color scheme `blues' for shading \showmembrane % Show the membrane \membranecolors{Black}{White} % as black lines w/o filling \labeloutside{extra} % Label extracellular side with `extra' \labelinside{intra} % Label intracellular side with `intra' \rulethickness{0.5pt} % Set thickness of label rules to 0.5pt \countercolor{Red} % Use red color for position counter \helixstyle{perspective} % Draw helical wheels in perspective \showbonds % Show bonds on helical wheels \hidemoment % Do not show hydrophobic moment \momentcolor{Lavender} % Lavender color for hydrophobic moment \scalemoment{100} % Moment rule length is 100% \showwheelnumbering % Show residue numbers on helical wheels \scalewheel{100} % Show full size helical wheel \symbolsize{medium} % Use medium sized symbols in wheels \donotshadestartMet % Do not shade the start methionine \showNterm % Show amino terminus as NH2 \showCterm % Show carboxy terminus as COOH \setfamily{labels}{sf} % Use sans serif family for labels \setseries{labels}{md} % Use normal series for labels \setshape {labels}{up} % Use upright shape for labels \setfamily{membranelabels}{sf} % Use sans serif for membrane labels \setseries{membranelabels}{md} % Use normal series for membrane labels \setshape {membranelabels}{up} % Use upright shape for membrane labels \setfamily{looplabels}{sf} % Use sans serif for loop labels \setseries{looplabels}{bf} % Use bold face for loop labels \setshape {looplabels}{up} % Use upright shape for loop labels \looplabelcolor{Red} % Set loop label color to `Red' \setfamily{TMlabels}{sf} % Use sans serif for TM labels \setseries{TMlabels}{bf} % Use bold face for TM labels \setshape {TMlabels}{up} % Use upright shape for TM labels \TMlabelcolor{Blue} % Set TM label color to `Blue' \labelTMs{\Romancount} % Label the TMs with roman numbers \setfamily{legend}{sf} % Use sans serif font for legend texts \setseries{legend}{md} % Use normal series for legend texts \setshape {legend}{up} % Use upright shape for legend texts \setsize {legend}{normalsize} % Use normal font size for legends \legendcolor{Black} % Set legend text color to `Black' \showlegend % Show the legend \hidegrid % Do not show the grid \labelstyle{CONFLICT} % Label style definitions for {diamond}{Black}{Blue}{White} % {Conflicting reports in literatur} % SwissProt data files \labelstyle{VARIANT} % | {diamond}{Black}{Orange}{Black} % | {Sequence variants} % V \labelstyle{VARSPLIC} % {diamond}{Black}{Apricot}{Black} % {Splice variants} % \labelstyle{MUTAGEN} % {diamond}{Black}{Red}{White} % {Mutation sites} % \labelstyle{SIGNAL} % {square}{Black}{Yellow}{Black} % {Signal peptide} % \labelstyle{TRANSIT} % {square}{Black}{Green}{Black} % {Transit peptide} % \labelstyle{PROPEP} % {square}{Black}{Red}{White} % {Propeptide} % \labelstyle{CHAIN} % {circ}{Black}{Aquamarine}{Blue} % {Polypeptide chain} % \labelstyle{PEPTIDE} % {circ}{Black}{Peach}{Black} % {Released peptide} % \labelstyle{DOMAIN} % {circ}{Black}{Turquoise}{Black} % {Domain} % \labelstyle{CABIND} % {circ}{Black}{Gray50}{White} % {Calcium binding domain} % \labelstyle{DNABIND} % {circ}{Black}{YellowGreen}{Black} % {DNA binding domain} % \labelstyle{NPBIND} % {circ}{Black}{Melon}{Black} % {Nucleotide phosphate binding} % \labelstyle{ZNFING} % {circ}{Black}{Lavender}{Black} % {Zinc finger} % \labelstyle{SIMILAR} % {circ}{Black}{SpringGreen}{Black} % {Similar region} % \labelstyle{REPEAT} % {circ}{Black}{Plum}{White} % {Sequence repeat} % \labelstyle{SITE} % {circ}{Black}{ForestGreen}{White} % {Special site} %