Export PDF

Multiple sequence alignments can be exported to PDF and with the LaTeX extension TeXshade written by Eric Beitz (see , http://www.pharmazie.uni-kiel.de/chem/Prof_Beitz/texshade.htm).

Installation
LaTeX is required. It provides the two shell commands "latex" and "pdflatex" which will be run by Strap. A graphical front end is not needed.

Exporting the sequence alignment to PDF
By pushing "Generate PDF" in the main card of the TeXshade-Dialog, two files are generated: The LaTeX file with ending .ps and the alignment file with ending .msf. These two files are then processed by the command pdflatex. The result is a pdf file. As soon as the pdf file exists, the "PDF" button to start the PDF viewer becomes active. The file path of pdflatex and of the PDF viewer can be customized.

Including the Alignment in Text-processor documents
Modern textprocessors allow insertion of PDF or Encapsulated PostScript images. For PostScript output, the respective check-box needs to be activated. Subsequently, the PostScript file (Suffix .ps) needs to be converted to Encapsulated PostScript (File suffix .eps) as described in "How do I convert PostScript to EPS?" of page http://www.postscript.org/FAQs/language/ .

Annotations
Residue selections can contain one or more annotations labeled with Texshade. Those entries usually contain the variables "PROTEIN" and "RESIDUES" which stand for the current protein number and the sequence positions.
Useful TeXshade-expressions which can be added to selections 
  \feature{top}{PROTEIN}{RESIDUES}{box[Red]}{peptide}
  \feature{ttop}{PROTEIN}{RESIDUES}{box[Red]}{peptide}
  \feature{bottom}{PROTEIN}{RESIDUES}{fill:$\uparrow$}{$S_{129}$}
  \feature{bbottom}{PROTEIN}{RESIDUES}{fill:X}{cleavage}
  \fingerprint{300}
TeXshade examples with variables 
   \feature{bottom}{PROTEIN}{RESIDUES}{fill:$\uparrow$}{$$FIRST_Aaa_{$FIRST_INDEX}$}
   \feature{bottom}{PROTEIN}{RESIDUES}{fill:$\uparrow$}{$$FIRST_A_{$FIRST_INDEX}$}
A detailed description is found on the TeXshade home page.

Plotting
Numeric values computed for each residue with a class ValueOfResidue can be plotted along the sequence alignment. Classes implementing ValueOfResidue have a getValues-method which returns a numeric value for each residue. The user chooses a class in the "plotting"-card IC_PLOT. The plot has four alternative locations: top, bottom, ttop, bbottom.

Fixing LaTeX-errors
Like in any programming language PDF-LaTeX stops when the text contains syntax errors. LaTeX reports the line number where the error occurred. For example 1.42 indicates an error at line 42. Typically the error is an incorrect TeXshade command assigned by the user to a residue annotation. The most frequent errors are unbalanced parentheses or characters that have a special syntactical meaning like underscore or "%".

Memory limitation: With large alignments the pdflatex-run may terminate with an ... memory exceeded ...-error. No PDF-output would be generated. If this happens the LaTeX heap size must be increased. Miktex users should set pdf_mem_size to a higher values in the file miktex.ini. For other LaTeX systems the memory settings in texmf.cnf must be increased ( e.g. multiplied by 10) and the program fmtutil run as root. Typical locations of the texmf.cnf are /etc/texmf/texmf.cnf /usr/share/texmf/web2c/texmf.cnf and /usr/local/teTeX/share/texmf/web2c/texmf.cnf. 
 # fmtutil  --byfmt=pdflatex