Scenes
delete *
load /Users/Tassos/ATX/Figures/for_figure.pdb, oatx
hide everything
create atx, (!(chain Y))
select smd1, (i;54-97)
select smd2, (i;98-142)
select smlink, (i;143-162)
select npp, (i;163-535)
select biglink, (i;536-569)
select biglink2, (i;570-605)
select nuc, (i;606-859)
color grey80, atx
show cartoon, atx
deselect all
set_view (\
-0.568654180, 0.556042552, -0.606175482,\
-0.678747773, 0.099114932, 0.727652967,\
0.464686513, 0.825223207, 0.321051002,\
0.000000000, -0.000000000, -1500.264526367,\
-4.860126495, 51.027359009, 32.698081970,\
1442.276489258, 1558.252563477, -20.000000000 )
scene 001,store
set_view (\
-0.679482639, 0.732202470, -0.046714969,\
-0.534882367, -0.450776666, 0.714634836,\
0.502198458, 0.510568380, 0.697938561,\
0.000000000, -0.000000000, -302.398071289,\
-4.860126495, 51.027359009, 32.698081970,\
244.410095215, 360.386169434, -20.000000000 )
scene 002, store
set_view (\
-0.680368483, 0.731592894, -0.043243695,\
-0.533085763, -0.453543991, 0.714226246,\
0.502909064, 0.508989036, 0.698580205,\
0.000000000, 0.000000000, -80.655578613,\
25.086999893, 70.416000366, 20.063999176,\
28.466300964, 132.844772339, -20.000000000 )
color violet, smd1
scene 003, store
set_view (\
-0.680368483, 0.731592894, -0.043243695,\
-0.533085763, -0.453543991, 0.714226246,\
0.502909064, 0.508989036, 0.698580205,\
0.000000000, 0.000000000, -90.347587585,\
12.055000305, 84.375000000, 5.337999821,\
38.158279419, 142.536712646, -20.000000000 )
color lightmagenta, smd2
scene 004, store
color slate, npp
create metals, (r;ZN,PO4 & oatx)
color green, (e;ZN)
show nb_spheres, metals
show sticks, metals
set non_bonded_size, 0.5
set_view (\
-0.400173873, 0.892436504, 0.208383337,\
-0.693620503, -0.443555415, 0.567589402,\
0.598962188, 0.082595684, 0.796509504,\
-0.000286847, -0.000187390, -142.273590088,\
5.206866264, 67.907577515, 35.451084137,\
81.553031921, 203.055847168, -20.000000000 )
scene 005, store
color lime, nuc
set_view (\
-0.621879756, 0.061470062, 0.780701756,\
-0.782621622, -0.084291324, -0.616772532,\
0.027890427, -0.994546652, 0.100527577,\
-0.000250248, -0.000290364, -147.368072510,\
-21.666936874, 33.136116028, 39.942222595,\
80.531028748, 214.184143066, -20.000000000 )
scene 006, store
color orange, biglink
color green, biglink2
color cyan, smlink
create allcys, (r;"Cys" & oatx & !(n;CA,C,O))
color yellow, (allcys & e;S)
show sticks, allcys
set_view (\
-0.376719087, -0.263238579, -0.888144970,\
-0.769845545, 0.622215331, 0.142124355,\
0.515198588, 0.737271130, -0.437051535,\
-0.000276916, 0.000880040, -269.698059082,\
-12.910985947, 50.231029510, 28.398471832,\
180.747894287, 358.640167236, -20.000000000 )
scene 007, store
set_view (\
-0.400173873, 0.892436504, 0.208383337,\
-0.693620503, -0.443555415, 0.567589402,\
0.598962188, 0.082595684, 0.796509504,\
-0.000244856, -0.000186650, -255.377792358,\
0.166468620, 61.978126526, 41.011249542,\
195.277618408, 315.565307617, -20.000000000 )
scene 008, store
show surface, atx
scene 009, store
set_view (\
-0.680854678, 0.365499586, 0.634713411,\
0.062925085, -0.834200501, 0.547874510,\
0.729717672, 0.412953436, 0.544967175,\
-0.000045636, -0.000450790, -48.652130127,\
12.492940903, 66.397384644, 34.894573212,\
-17.382667542, 114.933753967, -20.000000000 )
scene 010, store
set_view (\
-0.831421614, 0.518292010, -0.200318471,\
-0.354664981, -0.217471868, 0.909361362,\
0.427743167, 0.827097297, 0.364630610,\
-0.000045636, -0.000450790, -48.652130127,\
12.492940903, 66.397384644, 34.894573212,\
-17.382667542, 114.933753967, -20.000000000 )
scene 011, store
set_view (\
0.684314489, 0.168569282, 0.709445179,\
0.602257550, 0.417863816, -0.680214643,\
-0.411109507, 0.892743468, 0.184426919,\
0.000190429, 0.000882812, -259.116546631,\
2.908978462, 42.986923218, 37.205574036,\
151.476989746, 366.726684570, -20.000000000 )
scene 012, store
mset 1 x1250
- then we define the camera waypoints
scene 001, animate=0
mview store, 1
scene 002, animate=0
mview store, 50
scene 003, animate=0
mview store, 150
scene 004, animate=0
mview store, 250
scene 005, animate=0
mview store, 350
turn y, -25
mview store, 400
turn y, 50
mview store, 500
turn y, -25
mview store, 550
scene 006, animate=0
mview store, 650
scene 007, animate=0
mview store, 750
scene 008, animate=0
mview store, 850
from math import sin,pi
set transparency, 1.0
scene 009, animate=0
mview store, 851
for i in range(850,900): cmd.mdo( i, "set transparency, %f" %(math.cos(math.pi*(i-850)/100) ) )
scene 009, animate=0
mview store, 900
set transparency, 0.0
scene 010, animate=0
mview store, 1000
turn y, 20
mview store, 1025
turn y, -40
mview store, 1075
turn y, 30
mview store, 1100
scene 011, animate=0
mview store, 1125
turn y, 40
mview store, 1150
for i in range(1150,1200): cmd.mdo( i, "set transparency, %f" %(math.sin(math.pi*(i-1150)/100) ) )
scene 009, animate=0
mview store, 1200
scene 012, animate=0
mview store, 1250
- now we interpolate
mview interpolate
- and play the movie
rewind
mplay