Ticket #5311: command-file.cxc

# Load map and model
open emdb:13065 7otq

# Adjust map contour level and remove speckles
# Contour level of 0.15 is a good compromise because it shows that we have secondary structure resolution and also shows connected density at the H4 tail
volume #1 level 0.15
surface dust #1 size 10

# 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

# 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 ALC1 /k
name NATPase /k:42-266
name CATPase /k:267-500
name H4tail /b:16-24

# Apply color code
color H3 blue
color H4 green
color H2A yellow
color H2B red
color DNA silver
color ALC1 deeppink
color NATPase salmon

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

# Adjust display of atomic model
hide atoms
hide cartoons
cartoon style protein modeHelix tube radius 2 sides 24

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

# Movie: grey map, fade to map colored by chain assignment, fade to atomic model
view disc
view #1
movie record
wait 240
# Smooth transition from grey map to colored map
crossfade 120
color zone #1 near #2 distance 10
wait 240
# Smooth transition from map to atomic model
crossfade 120
hide #1
show cartoons
wait 240
movie stop
movie encode framerate 60 output wrong-result.mp4