%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% %%%%% Default parameter settings for the LaTeX ``TeXshade'' package %%%%% %%%%% %%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% %%%%% This example file contains all standard settings of the TeXshade %%%%% %%%%% package. It can be used as a template for the creation of perso- %%%%% %%%%% nal parameter files. All TeXshade user commands are allowed and %%%%% %%%%% functional when specified here. %%%%% %%%%% %%%%% %%%%% To activate these settings for your alignment load this file by %%%%% %%%%% naming it as optional parameter at the beginning of the texshade %%%%% %%%%% environment, e.g. %%%%% %%%%% %%%%% %%%%% \begin{texshade}[myparameterfile]{alignmentfile} %%%%% %%%%% . %%%%% %%%%% . %%%%% %%%%% \end{texshade} %%%%% %%%%% %%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \shadingmode{identical} % Shade identical residues only \shadingcolors{blues} % Select the blue color scheme for shading \constoallseqs % Calculate consensus considering all seqs \threshold{50} % Consensus threshold percentage is 50 \residuesperline{999} % As many residues as possible per line \numberingwidth{9999} % Assign space for 4 digit numbering \charstretch{1} % Do not stretch character width \linestretch{1} % Do not stretch lines vertically \gapchar{.} % . is printed in sequence gaps \gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt \gapcolors{Black}{White} % Gap symbols appear `Black on White' \domaingaprule{1pt} % If a rule is set between domains use 1 pt \domaingapcolors{Red}{White} % Domain separation line appears `Red on White' \numberingcolor{Black} % Numbering color is `Black' \shownumbering{right} % Show sequence numbering on the left \namescolor{Black} % Names' color is `Black' \featurenamescolor{Black} % Feature names' color is `Black' \featurestylenamescolor{Black} % Feature names' color is `Black' \shownames{left} % Show sequence names on the right \consensuscolors{Black}{White} % All consensus symbols/letters {Black}{White} % appear `Black on White' {Black}{White} % \showconsensus{bottom} % Show consensus line at bottom with \hidesequencelogo % Do not show a sequence logo as consensus \showlogoscale{leftright} % Show vertical scale bar if logo is on \logostretch{1} % Do not stretch sequence logo vertically \hidesubfamilylogo % Do not show a subfamily logo \subfamilythreshold{50} % Set subfamily threshold to 50% \shownegatives % Show negative values in subfamily logo \showrelevance[Black]{*} % Label relevant subfamily deviations \defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match \showleadinggaps % Show gap symbols before sequence start \rulercolor{Black} % Ruler's color is `Black' \hideruler % Do not show the ruler \rulersteps{10} % Ruler ticks every 10 residues \legendcolor{Black} % Legend text color is `Black' \hidelegend % Do not show the legend \alignment{center} % Center alignment on page \medsepline % Medium height if separation line is on \medblockskip % Medium skip between sequence blocks \flexblockspace % Use optimized space between blocks \featurerule{0.5ex} % Set feature rule thickness to 1/2 ex \bargraphstretch{1} % Do not stretch bars in feature graphs \colorscalestretch{1} % Do not stretch color scales in features \backtranstext{horizontal} % Horizontal triplets in feature texts \backtranslabel{alternating} % Alternating triplets in feature styles \setfamily{residues}{tt} % Use typewriter family for residues \setseries{residues}{md} % Use normal series for residues \setshape {residues}{up} % Use upright shape for residues \setsize {residues}{normalsize} % Use normal size for residues \setfamily{numbering}{tt} % Use typewriter family for numbering \setseries{numbering}{md} % Use normal series for numbering \setshape {numbering}{up} % Use upright shape for numbering \setsize {numbering}{normalsize} % Use normal size for numbering \setfamily{names}{tt} % Use typewriter family for names \setseries{names}{md} % Use normal series for names \setshape {names}{up} % Use upright shape for names \setsize {names}{normalsize} % Use normal size for names \setfamily{featurenames}{tt} % Use typewriter family for feature names \setseries{featurenames}{md} % Use normal series for feature names \setshape {featurenames}{up} % Use upright shape for feature names \setsize {featurenames}{normalsize}% Use normal size for feature names \setfamily{featurestylenames}{tt} % Use typewriter family for feature style names \setseries{featurestylenames}{md} % Use normal series for feature style names \setshape {featurestylenames}{up} % Use upright shape for feature style names \setsize {featurestylenames}{normalsize}% Use normal size for feature style names \setfamily{features}{rm} % Use roman family for feature texts \setseries{features}{md} % Use normal series for feature texts \setshape {features}{it} % Use italics shape for feature texts \setsize {features}{normalsize} % Use normal size for feature texts \setfamily{featurestyles}{tt} % Use typewriter family for feature styles \setseries{featurestyles}{md} % Use normal series for feature styles \setshape {featurestyles}{up} % Use upright shape for feature styles \setsize {featurestyles}{normalsize}% Use normal size for feature styles \setfamily{legend}{tt} % Use typewriter family 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 size for legend texts \setfamily{ruler}{sf} % Use sans serif font for ruler numbers \tintdefault{medium} % Use medium tint intensity \emphdefault{it} % Use italics to emphasize regions \showonPHDsec{alpha,beta} % Show helices and strands (PHD input) \showonPHDtopo{internal,external,TM}% Show int., ext. and TM's (PHD input) \showonHMMTOP{TM} % Show TM's (not int/ext on HMMTOP input) \showonSTRIDE{alpha,3-10,pi,beta} % Show helices and strands (STRIDE input) \showonDSSP{alpha,3-10,pi,beta} % Show helices and strands (DSSP input) \secondcolumnDSSP % Use numbering from 2. column in DSSP \appearance{PHDtopo}{internal} % \ {bottom}{'-'} % \ {int.\ \Alphacount} % | \appearance{PHDtopo}{external} % | {top}{,-,} % | {ext.\ \Alphacount} % | \appearance{PHDtopo}{TM}{top} % | {box[LightGray]:TM\numcount}{} % | \appearance{HMMTOP}{internal} % | {bottom}{'-'} % | {int.\ \Alphacount} % | \appearance{HMMTOP}{external} % | {top}{,-,} % | {ext.\ \Alphacount} % | \appearance{HMMTOP}{TM}{top} % | {helix}{TM\numcount} % | \appearance{PHDsec}{alpha}{top} % | {box:$\alpha$\numcount}{} % | \appearance{PHDsec}{beta}{top} % | {-->}{$\beta$\numcount} % | \appearance{STRIDE}{alpha}{top} % | {box:$\alpha$\numcount}{} % | Definitions for the appearance of \appearance{STRIDE}{3-10}{top} % \ {fill:$\circ$}{3$_{10}$} % > secondary structures included from| \appearance{STRIDE}{pi} % / {top}{---}{$\pi$} % | PHD-, STRIDE-, or DSSP-files. \appearance{STRIDE}{beta}{top} % | {-->}{$\beta$\numcount} % | \appearance{STRIDE}{bridge} % | {top}{fill:$\uparrow$}{} % | \appearance{STRIDE}{turn} % | {top}{,-,}{turn} % | \appearance{DSSP}{alpha}{top} % | {box:$\alpha$\numcount}{} % | \appearance{DSSP}{3-10}{top} % | {fill:$\circ$}{3$_{10}$} % | \appearance{DSSP}{pi} % | {top}{---}{$\pi$} % | \appearance{DSSP}{beta}{top} % | {-->}{$\beta$\numcount} % | \appearance{DSSP}{bridge} % | {top}{fill:$\uparrow$}{} % | \appearance{DSSP}{turn} % | {top}{,-,}{turn} % | \appearance{DSSP}{bend}{top} % / {fill:$\diamond$}{} % / \pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity \pepsims{F}{YW} % Y and W are similar to F \pepsims{Y}{WF} % W and F are similar to Y \pepsims{W}{YF} % Y and F are similar to W \pepsims{I}{LVM} % L, V and M are similar to I \pepsims{L}{VMI} % V, M and I are similar to L \pepsims{V}{MIL} % M, I and L are similar to V \pepsims{R}{KH} % K and H are similar to R \pepsims{K}{HR} % H and R are similar to K \pepsims{H}{RK} % R and K are similar to H \pepsims{A}{GS} % G and S are similar to A \pepsims{G}{A} % A (but not S) is similar to G \pepsims{S}{TA} % T and A are similar to S \pepsims{T}{S} % S (but not A) is similar to T \pepsims{D}{EN} % E and N (but not Q) are similar to D \pepsims{E}{DQ} % D and Q (but not N) are similar to E \pepsims{N}{QD} % Q and D (but not E) are similar to N \pepsims{Q}{NE} % N and E (but not D) are similar to Q \DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity \DNAsims{A}{GR} % G and R are similar to A \DNAsims{G}{AR} % A and R are similar to G \DNAsims{R}{AG} % A and G are similar to R \DNAsims{C}{TY} % T and Y are similar to C \DNAsims{T}{CY} % C and Y are similar to T \DNAsims{Y}{CT} % C and T are similar to Y