Multiple sequence alignments can be exported to PDF and with the
written by Eric Beitz (see , http://www.pharmazie.uni-kiel.de/chem/Prof_Beitz/texshade.htm).
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
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.
Useful TeXshade-expressions which can be added to selections
A detailed description is found on the TeXshade home page.
TeXshade examples with variables
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 .
The plot has four alternative locations: top, bottom, ttop, bbottom.
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 "%".
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
# fmtutil --byfmt=pdflatex