TeXshade example generated by STRAP
PACKAGE:charite.christo.strap. The following listing contains a LaTeX-TeXshade file for a multiple sequence alignment of proteasomal sequences generated with STRAP. Only in case of errors the user needs to inspect the LaTeX file. The first 10 lines are concerned with the geometry of the paper. Line 13 refers to the multiple sequence file alignm.msf. Lines 20-37 replace the names in the alignment row header. The user has chosen to take the WIKI:Protein_structure#Secondary_structure definition from protein a1_1ryp to generate red and yellow bars for helices and sheets (line 32-33). The sequence of protein a1_1ryp is not shown (line 34). Line 15 is a comment because it starts with a "%". Removing the "%" the line is uncommented and "fingerprint" is switched on. Lines 28-30 were taken from affiliations of named selections of proteins (ResidueAnnotations). For example line 28 was generated because the residue selection of protein b1_SaccharomycesCerevisiae contains a TeXshade entry \feature{bottom}{PROTEIN}{RESIDUES} {fill:$\uparrow$}{$T_{1}$(active site)}.
  1 \documentclass[pdftex,nopagenumbering]{letter}
  2 \usepackage{texshade}
  3 \usepackage{hyperref}
  4 \setlength{\topmargin}{-20mm}
  5 \setlength{\headheight}{0mm}
  6 \setlength{\headsep}{0mm}
  7 \setlength{\topskip}{0mm}
  8 \setlength{\paperheight}{205mm}
  9 \setlength{\paperwidth}{230mm}
 10 \setlength{\oddsidemargin}{0mm}
 11 \begin{document}
 12 \pagestyle{empty}
 13 \begin{texshade}{strapOut/alignm.msf}
 14 \residuesperline*{58}
 15 %\fingerprint{300}
 16 %\hidenumbering
 17 \shadingmode{similar}
 18 \hideconsensus
 19 \shownames{left}
 20 \nameseq{1}{$\alpha_1$ SacSe} % a1_1ryp.dssp.gz
 21 \nameseq{2}{$\alpha_1$ SacSe} % a1_SaccharomycesC
 22 \nameseq{3}{$\beta_1$ SacSe} % b1_SaccharomycesC
 23 \nameseq{4}{E.coli} % hs_Ecoli.dssp
 24 \nameseq{5}{Plasmodium} % Hs_PlasmodiumFalciparu
 25 \nameseq{6}{Leishmania} % hs_LeishmaniaMajor_36.
 26 \nameseq{7}{Trypanosoma} % hs_Trypanosoma_Brucei
 27 \nameseq{8}{E.Coli} % hs_EscherichiaColi.swiss
 28 \feature{bottom}{3}{20..20}{fill:$\uparrow$}
     {$T_{1}$(active site)} % b1_SaccharomycesCerevisiae
 29 \feature{bottom}{3}{52..52}{fill:$\uparrow$}
     {$K_{33}$(active site)} % b1_SaccharomycesCerevisiae
 30 \feature{bottom}{3}{148..148}{fill:$\uparrow$}
     {$S_{129}$(active site)} % b1_SaccharomycesCerevisiae
 31 % DSSP
 32 \feature{top}{1}{16..24,77..98,104..120,165..179,
    189..204,228..239}{box[Red]}{helix}  % a1_1ryp.d
 33 \feature{top}{1}{32..36,41..46,62..64,70..74,130..137,
    153..155,158..161,213..219,222..225}{box[Yellow]}{sheet}
 34 \hideseq{1} % a1_1ryp.dssp.gz
 35 \end{texshade}
 36 \end{document}
SEE_DIALOG:DialogExportAlignment SEE_CLASS:ResidueAnnotation SEE_CLASS:AddAnnotation