Export PDF

[Menu-bar>Protein>File>Export proteins and alignments] Multiple sequence alignment 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). For simple alignment output the Export alignment ... is easier to use. Applying TeXshade requires some basic knowledge about type setting. Novices may have a look at the tiny introduction * .

Installation
A LaTeX system is required. LaTeX provides the two shell commands "latex" and "pdflatex". Windows users may use the in . Another option is . A basic Miktex installation is sufficient and the full installation is not required. After installation of Miktex please re-login or restart the computer. Macintosh users may install .

Exporting the sequence alignment to PDF
The main card of the TeXshade-Dialog has three buttons Texshade#BUT_LAB_Source, Texshade#BUT_LAB_RunTex and Texshade#BUT_LAB_Pdf which need to be pressed one after the other. On pressing Texshade#BUT_LAB_Source two files are generated: a * LaTeX-file and a multiple sequence file. As soon as both files exist the button Texshade#BUT_LAB_RunTex becomes active. When it is pressed the program pdflatex starts to work on these two files. The result is a PDF-document which will be displayed when the button Texshade#BUT_LAB_Pdf is pressed.

Including the Alignment in Text-processor documents
PDF graphics can usually not be included into MS-Word or Openoffice documents. But PostScript figures can. The check-box to toggle PDF and PostScript becomes accessible by clicking Texshade#BUT_LAB_Source with the CTRL key. STRAP will use the command latex instead of pdflatex. The output is a .ps file which needs to be converted to .eps as described in "How do I convert PostScript to EPS?" of page http://www.postscript.org/FAQs/language/ .

Annotations
Residue annotations can contain one or more fields labeled with Texshade. Those entries usually contain the variables "PROTEIN" and "RESIDUES" which are replaced by the positions and the protein number.
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. In this case cryptic messages are written to stderr and no PDF is produced. LaTeX reports the line number where the error occurred like 1.42 meaning that an error was found 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 "%".

Customization: In the customize dialog you can specify the command for pdflatex and for the pdf viewer.

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