• alignment.html which is the alignment document. It is an HTML file which can be displayed in any modern browser. The recommended browser is Google-Chrome.
• The JavaScript-file with the ending ".js" which is the complete run-time library needed by the alignment file.
• exampleFixedSize.html: Example HTML code for embedding the alignment into another web document. Here, the alignment panel has a fixed size. If the alignment size exceeds the panel size, then scroll-bars appear.
• exampleDynamicSize.html: Example HTML code where the size of the alignment panel is maximized according to the current window size of the browser.

#/home/people/christo/public_html/strap/AA2/tmp/apache/x5a0743dd12_fb88/command.txt
JS="-javaScript=http://www.bioinformatics.org/strap/AA2/toHTML003.js toHTML004.js"
streams=" -stdout=stdout.txt -stderr=stderr.txt"
cd /home/people/christo/public_html/strap/AA2/tmp/apache/x5a0743dd12_fb88/
aaJavaopt=" -DwritePID=pidj.txt  -jar -Djava.awt.headless=true -Duser.home=/home/people/christo/public_html/strap/AA2/tmp/apache/"
aaJar=/home/people/christo/public_html/strap/AA2/strap.jar
export PATH=/home/people/christo/public_html/strap/AA2/bin/:/home/people/christo/public_html/strap/AA2:$PATH
PDB='-localPDB=/home/groups/groups/pdbmirror/data/structures/all/pdb/pdb????.ent.gz'
UNIPROT=-localSequenceDB=UNIPROT:/home/people/christo/public_html/strap/AA2/DB/uniprot_sprot.fasta.gz
PDBBLAT=-pdbBlat=/home/people/christo/public_html/strap/AA2/DB/pdb_seqres.txt
CSA=-CSA=/home/people/christo/public_html/strap/AA2/DB/CSA_2_0_121113.txt
java -DAA2_KANN_ABGEBROCHEN_WERDEN $aaJavaopt $JavaProxy $aaJar -nameFromFasta -writeWordCompletion -logURLs $streams $PDB $UNIPROT $PDBBLAT $CSA -a3d=tm_align $JS  -script14=s.strap -script0="load  PFAM:PF00941" -toHTML=ali.php

/home/people/christo/public_html/strap/AA2/AA2LockRun -L /home/people/christo/public_html/strap/AA2/tmp/apache/lock -W --printPID /home/people/christo/public_html/strap/AA2/tmp/apache/x5a0743dd12_fb88/pid.txt --printPID2 /home/people/christo/public_html/strap/AA2/tmp/apache/x5a0743dd12_fb88/pid2.txt -- sh /home/people/christo/public_html/strap/AA2/tmp/apache/x5a0743dd12_fb88/command.txt > /dev/null 2> /dev/null &

Script:
set_color_mode Charge
set_conservation_threshold 80
set_characters_per_line 60
align $OPT_IF_UNGAPPED *
export_mfa ali.mfa, *
project_coordinates AUTO  $OPT_SIDE_CHAIN_ATOMS , !$PROTEINS_FROM_STRUCTURE_FILE 
new_selection   */FAD , hetero, AROUND=FAD ANGSTROM=5
set_annotation  */FAD , Color, #3322FF
set_annotation  */FAD , Style, STYLE_BACKGROUND