## 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 . Those entries usually contain the variables "PROTEIN" and "RESIDUES" which stand for the current protein number and the sequence positions.
 ``` \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} ```
 ``` \feature{bottom}{PROTEIN}{RESIDUES}{fill:\$\uparrow\$}{\$\$FIRST_Aaa_{\$FIRST_INDEX}\$} \feature{bottom}{PROTEIN}{RESIDUES}{fill:\$\uparrow\$}{\$\$FIRST_A_{\$FIRST_INDEX}\$} ```
``` # fmtutil  --byfmt=pdflatex