Protein Explorer Animation Command Scripts for Lac:DNA Morphs

The scripts below can be pasted into the animation script box in the NMR Models/Animation control panel of Protein Explorer displaying the lac:DNA morph (1OSL model 9 to 1L1M model 14). Pressing the [Animate] button will generate an animation rendered and colored like the corresponding saved animation. The script can then be customized if desired.


Cartoon Script

  #--Begin color scheme--
## show selected false
select all
color red #to clear previous palette
select :a,:b
color structure
select :c
color yellow
select :d
color orange
  #--End color scheme--
#$ Begin animation loop
  #--Begin display script--
  #Hide ssbonds from previous model.
select all
ssbonds off
  #Main display.
select model=@ and nucleic
spacefill
select model=@ and protein
cartoon
  #Show ssbonds.
select model=@ and protein
ssbonds 0.25
set ssbonds backbone
color ssbonds [255,200,50]
  #--End display script--


Sticks Script

  #--Begin color scheme--
## show selected false
select all
color red #to clear previous palette
select :a
color magenta
select :b
color green
select :c
color yellow
select :d
color orange
  #--End color scheme--
#$ Begin animation loop
  #--Begin display script--
  #Hide ssbonds from previous model.
select all
ssbonds off
  #Main display.
select model=@ and nucleic
spacefill
select model=@ and protein
wireframe 0.2
  #Show ssbonds.
select model=@ and protein
ssbonds 0.25
set ssbonds backbone
color ssbonds [255,200,50]
  #--End display script--


Spacefill Script

  #--Begin color scheme--
## show selected false
select all
color red #to clear previous palette
select :a
color magenta
select :b
color green
select :c
color yellow
select :d
color orange
  #--End color scheme--
#$ Begin animation loop
  #--Begin display script--
  #Hide ssbonds from previous model.
select all
ssbonds off
  #Main display.
select model=@
spacefill
  #Show ssbonds.
select model=@ and protein
ssbonds 0.25
set ssbonds backbone
color ssbonds [255,200,50]
  #--End display script--


Contacts Script (with DNA dot surface)

# SPECIFIC BASE CONTACTS IN 1L1M:
  #--Begin color scheme--
## show selected false
select all
color red #to clear previous palette
select :a
color magenta
select :b
color green
select :c
color yellow
select :d
color orange
select (G13D.N2,Ala53A.O),(Tyr17A.OH,G8C.N7),(Tyr17B.OH,A14C.N7),(Arg22.NH2,G6.O6)
select selected or (hydrogen and within(1.2, selected))
color cpk
  #--End color scheme--
#$ Begin animation loop
  #--Begin display script--
  #Hide ssbonds from previous model.
select all
ssbonds off
dots off
  #Main display.
select model=@
wireframe 0
select model=@ and nucleic
dots 30
select model=@ and ((G13D.N2,Ala53A.O),(Tyr17A.OH,G8C.N7),(Tyr17B.OH,A14C.N7),(Arg22.NH2,G6.O6))
select selected or (model=@ and hydrogen and within(1.2, selected))
spacefill
  #Show ssbonds.
select model=@ and protein
ssbonds 0.3
set ssbonds backbone
color ssbonds [255,200,50]
  #--End display script--


Contacts Script (without DNA dot surface)

# SPECIFIC BASE CONTACTS IN 1L1M:
  #--Begin color scheme--
## show selected false
select all
color red #to clear previous palette
select :a
color magenta
select :b
color green
select :c
color yellow
select :d
color orange
select (G13D.N2,Ala53A.O),(Tyr17A.OH,G8C.N7),(Tyr17B.OH,A14C.N7),(Arg22.NH2,G6.O6)
select selected or (hydrogen and within(1.2, selected))
color cpk
  #--End color scheme--
#$ Begin animation loop
  #--Begin display script--
  #Hide ssbonds from previous model.
select all
ssbonds off
  #Main display.
select model=@
wireframe 0
select model=@ and ((G13D.N2,Ala53A.O),(Tyr17A.OH,G8C.N7),(Tyr17B.OH,A14C.N7),(Arg22.NH2,G6.O6))
select selected or (model=@ and hydrogen and within(1.2, selected))
spacefill
  #Show ssbonds.
select model=@ and protein
ssbonds 0.3
set ssbonds backbone
color ssbonds [255,200,50]
  #--End display script--