# Load model
open 7otq

# Name orientations to make it easier to come back to them

## Orient in disc view and zoom in to fill camera view
turn x -90
turn z -5
view #1
view name disc

## Orient in dyad view
view disc
turn x 90
turn z -5
turn x -5
view name dyad

## Orient in gyres view
view dyad
turn x 180
turn z -5
view name gyres

## Orient to look at H4 tail
view gyres
turn y 95
turn x 45
turn y 30
view name H4tailInteraction
view H4tailInteraction
turn y -50
turn x -15
turn y -5
view name H4tailInteraction2

# Find correct protein secondary structure assignments in atomic model
dssp protein

# Load other PDB entries to compare to
## Yeast Snf2 in apo, ADP-BeFx and ADP bound states
open 5z3l
open 5z3u
open 5z3o
## Yeast Isw1 in ADP-BeFx and ADP bound states
open 6jyl
open 6iro
## Human CHD4 in ADP-BeFx bound state
open 6ryr

# Align them all to our model, based on H3 chains
mmaker #2-7/a,e to #1/a,e

# Name chains to make the rest easier to read
name H3 /a/e
name H4 /b/f
name H2A /c/g
name H2B /d/h
name histones /a-h
name DNA /i/j
name mainNuc #1/a-j
name otherNucs #2-7/a-j
name ALC1 #1/k
name NATPase #1/k:42-266
name CATPase #1/k:267-500
name H4tail #1/b:16-24
name Snf2Apo #2/o
name Snf2ADPBeF #3/o
name Snf2ADP #4/o
name Snf2 #2-4/o
name Snf2NATPase #2-4/o:670-1000
name Isw1ADPBeF #5/k
name Isw1ADP #6/l
name Isw1 #5/k#6/l
name Isw1NATPase #5/k:101-417#6/l:101-417
name CHD4 #7/w:727-1212
name CHD4NATPase #7/w:446-960
name bindingFactors #1/k#2-4/o #5/k#6/l #7/w:727-1212

# Apply color code
color H3 blue
color H4 green
color H2A yellow
color H2B red
color DNA silver
color ALC1 deeppink
color NATPase salmon
color Snf2 teal
color Snf2NATPase turquoise
color Isw1 dodgerblue
color Isw1NATPase skyblue
color CHD4 limegreen
color CHD4NATPase greenyellow

# Global display options
set bgColor white
lighting soft
graphics silhouettes true

# Adjust display of atomic models
hide atoms
hide cartoons
show mainNuc cartoons
show bindingFactors cartoons
hide #!2-7 models
transparency mainNuc 75 target c
cartoon style protein modeHelix tube radius 2 sides 24

view gyres

# Make figures
## Superimposition of Snf2Apo
show #!2 models
save ALC1-Snf2Apo_superimposition_gyres-view.png transparentbackground true supersample 3
hide #!2 models
## Superimposition of Snf2ADPBeF
show #!3 models
save ALC1-Snf2ADPBeF_superimposition_gyres-view.png transparentbackground true supersample 3
hide #!3 models
## Superimposition of Snf2ADP
show #!4 models
save ALC1-Snf2ADP_superimposition_gyres-view.png transparentbackground true supersample 3
hide #!4 models
## Superimposition of IswADPBeF
show #!5 models
save ALC1-Isw1ADPBeF_superimposition_gyres-view.png transparentbackground true supersample 3
hide #!5 models
## Superimposition of IswADP
show #!6 models
save ALC1-Isw1ADP_superimposition_gyres-view.png transparentbackground true supersample 3
hide #!6 models
## Superimposition of CHD4ADPBeF
show #!7 models
save ALC1-CHD4ADPBeF_superimposition_gyres-view.png transparentbackground true supersample 3
#hide #!7 models