Sample script to prepare PNGs for animated gif of an elnemo mode

createPNGs.pml

##Thanks to Hemochromatosis journal for help
load ../../../2GK1A_NGTdeleted_referenceorientation.pse, reference
load ./1207270221251193.7.pdb, modes
align modes, 2GK1A_NGTdeleted
zoom 2GK1A_NGTdeleted, buffer=-8.5
delete 2GK1A_NGTdeleted

#Create secondary structure annotation for elnemo output
dss modes

#Representations and colouring
hide everything, all
show cartoon, modes
select firstDomain, resi 1-167
select secondDomain, not firstDomain
color red, firstDomain
color blue, secondDomain

##Create pngs of movie
#Iterate from 1 .. 11 then 10 .. 2
mset 1 -11 -1
#viewport 400, 280
bg_color white
set ray_opaque_background, off
set ray_trace_frames, 1
set cache_frames=0
set ray_trace_mode, 0; # color raytrace, no outlines
set antialias, 2;   #High anti-aliasings
mclear
mpng mov