# BANNER TEXT
#bannerMessage = "Bacterial Flagellar Hook Protein - Comparison Between Species"
#bannerMessage2 = "Fadel Samatey Group"

# ARBITRARY COLOR KEYS
function arbitraryColorKeys()
{
	# Colors can be specified in various ways. Those below are specified
	# using Red-Green-Blue (RGB) hexadecimal values. Each color
	# can be between 00 and ff (255 in decimal).
	# See http://jmol.sourceforge.net/jscolors/
	
	colorKey("Salmonella (2004)", "white")
	colorKey("Campylobacter (2016)", "magenta")
}

# DEFINE BANNER, COLOR KEY FUNCTIONS
#script MPSupportVersion03.spt
if (_applet)
{
	script "/wiki/images/3/32/MPSupportVersion03.spt"
}
else
{
	script MPSupportVersion03.spt
}

# INITIALIZE
initializeBeforeEachCycle("nozap")

# LOAD MODELS
if (_applet)
{
	load "/wiki/images/e/e4/3a69-71-357.pdb.gz"
	load append "/wiki/images/5/5a/Workbench_3vi9_chain_b.pdb.gz"
	load append "/wiki/images/e/e4/3a69-71-357.pdb.gz"
}
else
{
	load 3a69-71-357.pdb.gz
	load append Workbench_3vi9_chain_b.pdb.gz # was FlgE79cj_monom.pdb
	load append 3a69-71-357.pdb.gz # for reference position to undo the alignment
}

# SHOW BANNER AT TOP (bannerMessage2 is defined in MPSupportVersion01.spt)
#showBannerAcrossTop(bannerMessage, bannerMessage2)

# SHOW ARBITRARY COLOR KEY(S)
#		echoFontSize = 12
		echoColorKeyFontSize = 13 # was 16
		
		colorKeyTopVertPct = 95 # was 80
		colorKeyLineHeightPct = 6

arbitraryColorKeys()

# = = = = = = = = = = = = = = = = = = = = = = = = = = =
# FIRST SCENE
#-------------------------------------------------------
#script MP3_orient.spt

#Follows Z-Y-Z convention for Euler angles
reset;center {-1.6160011 113.628006 65.1205}; rotate z 13.43; rotate y 115.4; rotate z -95.88; zoom 115.0; translate y 0.14; set rotationRadius 109.83;

select 1.1,3.1
translate selected 0 -20 70
rotate selected z 30
rotate selected y -90
rotate selected z -30

#-------------------------------------------------------
#script MP3_render1.spt

select all
wireframe off
spacefill off

backbone off

frame 2.1
isosurface s1 sasurface #this is quick!
color isosurface magenta translucent -1

frame all

select 1.1
color white
backbone 0.4
spacefill

select 3.1
backbone
color [x00ff00]

hide 3.1

#-------------------------------------------------------

delay 2
#-------------------------------------------------------
#script MP3_animate.spt

select all
rotate y 360 40 # spin 40 degrees/second

delay 4.5

#load 3a69-71-357.pdb
#load append FlgE79cj_monom.pdb

# AVERAGE ALIGNMENT FOR D1+D2
compare {1.1} {2.1} SUBSET {*.ca} ATOMS {71-165} {94-188} {166-357} {624-815} ROTATE TRANSLATE 

set spiny 30
spin on

#-------------------------------------------------------

delay 8

# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# SECOND SCENE
#-------------------------------------------------------
#script MP3_render2.spt

select all
wireframe off
#spacefill off
backbone 0.4

frame all

select 1.1
color white

select 2.1 and not water
#color [x00ff00]
color group


#-------------------------------------------------------
select 2.1
backbone off

delay 2

select 1.1
shrinkSpacefill()

delay 5

select 2.1
backbone 0.4

delay 2

isosurface s1 color translucent 6
delay 2

isosurface s1 color translucent 7
delay 2

isosurface s1 color translucent 8
delay 2

# ECHO RAINBOW CAMPYLOBACTER COLOR KEY
set echo keyEcho2
if (_applet)
{
	set echo image "/wiki/images/4/47/Campylobacter-rainbow.png"
}
else
{
	set echo image "Campylobacter-rainbow.png"
}

isosurface s1 delete
#-------------------------------------------------------

#script MP3_animate2.spt

spin on

delay 7

compare {1.1} {3.1} SUBSET {*.ca} ROTATE TRANSLATE

set spiny 30
spin on
delay 6

# average alignment for D1+D2
compare {1.1} {2.1} SUBSET {*.ca} ATOMS {71-165} {94-188} {166-357} {624-815} ROTATE TRANSLATE 

set spiny 30
spin on
#-------------------------------------------------------

delay 6
#-------------------------------------------------------

#script MP3_label_domains.spt

set echo dom1 {(94-168 or 744-819) and 2.1} # geometric center of atoms in residues by seq number
set echo dom1 left
echo "            D1"
font echo 24 bold sansserif
color echo white

set echo dom2 {(169-192 or 619-743) and 2.1} # geometric center of atoms in residues by seq number
set echo dom2 left
echo "            D2"
font echo 24 bold sansserif
color echo white

set echo dom3 {(193-260 or 441-618) and 2.1} # geometric center of atoms in residues by seq number
set echo dom3 left
echo "            D3"
font echo 24 bold sansserif
color echo white

set echo dom4 {(261-440) and 2.1} # geometric center of atoms in residues by seq number
set echo dom4 left
echo "            D4"
font echo 24 bold sansserif
color echo white
#-------------------------------------------------------

delay 4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CLOSEUP (ZOOM IN, ZOOM OUT)

spin off

# ZOOM IN 

moveto /* time, axisAngle */ 3.0 { 753 534 -385 132.61} /* zoom, translation */  201.14 -1.27 -30.17  /* center, rotationRadius */ {-1.6160011 113.628006 65.1205} 109.83 /* navigation center, translation, depth */ {0.0 0.0 0.0} -71.68843 -105.44254 0.0

spin on
delay 5
#-------------------------------------------------------
#script MP3_animate3.spt

# ALIGN D1
spin off
delay 1
compare {1.1} {2.1} SUBSET {*.ca} ATOMS {139} {160} {323} {785} {347} {809} ROTATE TRANSLATE 

set spiny 30
spin on
delay 6

# ALIGN D2
spin off
delay 1
compare {1.1} {2.1} SUBSET {*.ca} ATOMS {280} {740} {197} {641} {234} {688} ROTATE TRANSLATE 

set spiny 30
spin on
delay 6

spin off
delay 1
compare {1.1} {2.1} SUBSET {*.ca} ATOMS {71-165} {94-188} {166-357} {624-815} ROTATE TRANSLATE 

set spiny 30
spin on
#-------------------------------------------------------


delay 5

# ZOOM OUT TO STARTING POSITION

moveto /* time, axisAngle */ 3.0 { 753 534 -385 132.61} /* zoom, translation */  115.0 0.0 0.35  /* center, rotationRadius */ {-1.6160011 113.628006 65.1205} 109.83 /* navigation center, translation, depth */ {0.0 0.0 0.0} -34.885223 -36.977215 0.0;

delay 3

set echo bottom
echo Animation Completed