#!/usr/bin/strap-protein-alignment

# Number of characters per line
set_characters_per_line 24

# Emphasize residues conserved in 70% of all rows
set_conservation_threshold 70

# Color according to the chemical features of amino acids
set_color_mode charge


# The next two lines define the alignment

aa_sequence MVLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFP, Canus
aa_sequence -VLSAAERAQVKAAWGKI--QAGAHGAEALERMFLGFPTTKTYPF, Xenopus
aa_sequence MILSAAERAQIKAAWGKVG-NAGAHGAEALD--FLGYPTTKSYPY, Drosophila

# Xenopus starts with amino acid number 2
set_residue_index_offset 1, Xenopus


# The next line sets the secondary structure. H=helix, E=extended sheet

secondary_structure ---HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH-- , Canus




# Accession ID provides a link to a database

accession_id  UNIPROT:P0A7B8 , Canus


# With the command icon, the protein icon image is set

icon http://www.bioinformatics.org/strap/toHTML/data/dog_temp.gif, Canus
icon http://www.bioinformatics.org/strap/toHTML/data/Frog.gif, Xenopus
icon fly_temp.gif, Drosophila

balloon_text    Ein <b>Frosch</b>, Xenopus
balloon_text    If you do not like this sequence<br>you can move it to the trash bin with the mouse., Canus


# new_selection defines a new residue selection
# add_annotation or set_annotation adds information to the residue selection 


new_selection   Canus/activeSite, group_test, 11
set_annotation  Canus/activeSite, Hyperrefs, http://en.wikipedia.org/wiki/Active_site
set_annotation  Canus/activeSite, Style, STYLE_BACKGROUND
set_annotation  Canus/activeSite, Color, #ff0000
add_annotation  Canus/activeSite, Balloon, This residue is part of the active site

new_selection   Canus/a_selection, group_test, 2-18
set_annotation  Canus/a_selection, Hyperrefs, http://en.wikipedia.org/wiki/N-terminus
set_annotation  Canus/a_selection, Style, STYLE_BACKGROUND
set_annotation  Canus/a_selection, Color, #00ffFF
add_annotation  Canus/a_selection, Balloon, Another balloon message
add_annotation  Canus/a_selection, Balloon, This can be dragged with the mouse to the trash.



new_selection   Xenopus/my_1st_selection, group_test, 30-
set_annotation  Xenopus/my_1st_selection, Hyperrefs, http://www.charite.de
set_annotation  Xenopus/my_1st_selection, Style, STYLE_UNDERLINE
set_annotation  Xenopus/my_1st_selection, Color, #00ff01
add_annotation  Xenopus/my_1st_selection, Balloon, This is a selection.

 
new_selection   Xenopus/my_2nd_selection, group_test, 20-33 
set_annotation  Xenopus/my_2nd_selection, Hyperrefs, http://en.wikipedia.org/wiki/C-terminus
set_annotation  Xenopus/my_2nd_selection, Style, STYLE_UNDERLINE
set_annotation  Xenopus/my_2nd_selection, Color, #ff0000
add_annotation  Xenopus/my_2nd_selection, Balloon, This is another  selection. Drag it to the trash with the mouse.



project_coordinates 1QPW_A , Xenopus