package require http
# To run this script please run it in VMD as source script.vmd
# 
# If you find this tool useful for your work, please cite it as:
# Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C-M, Otyepka M, Koča J: MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminform. 2013, 5:39.
# 
proc add_atom {id center r} {
 set atom [atomselect top "index $id"]
 $atom set {x y z}  $center
 $atom set radius $r
}
set channel1 [mol new atoms 19]
mol top $channel1
animate dup $channel1
mol color ColorID 1
mol representation VDW 1 60
add_atom 0 {{ -7.568, -3.569, -5.216 }} 1.590
add_atom 1 {{ -7.037, -3.997, -5.948 }} 1.800
add_atom 2 {{ -6.198, -4.175, -6.242 }} 2.060
add_atom 3 {{ -5.618, -3.712, -6.767 }} 1.850
add_atom 4 {{ -5.147, -3.124, -7.424 }} 1.770
add_atom 5 {{ -4.481, -2.547, -7.433 }} 1.830
add_atom 6 {{ -3.582, -2.402, -7.846 }} 1.620
add_atom 7 {{ -2.825, -2.013, -8.286 }} 1.540
add_atom 8 {{ -2.088, -1.439, -8.618 }} 1.510
add_atom 9 {{ -1.275, -0.908, -8.858 }} 1.770
add_atom 10 {{ -0.609, -0.349, -8.832 }} 1.990
add_atom 11 {{ -0.011, 0.016, -8.140 }} 1.690
add_atom 12 {{ 0.724, 0.384, -7.571 }} 1.550
add_atom 13 {{ 1.471, 0.762, -7.089 }} 1.660
add_atom 14 {{ 2.391, 1.094, -7.299 }} 1.610
add_atom 15 {{ 3.153, 1.655, -7.461 }} 1.610
add_atom 16 {{ 3.786, 2.395, -7.660 }} 1.730
add_atom 17 {{ 4.280, 3.066, -7.166 }} 1.720
add_atom 18 {{ 5.152, 3.167, -6.870 }} 1.550
mol delrep 0 $channel1
mol addrep $channel1
mol selection {{all}}
mol rename top {channel1}


set channel2 [mol new atoms 16]
mol top $channel2
animate dup $channel2
mol color ColorID 2
mol representation VDW 1 60
add_atom 0 {{ -7.568, -3.569, -5.216 }} 1.590
add_atom 1 {{ -7.037, -3.997, -5.948 }} 1.800
add_atom 2 {{ -6.198, -4.175, -6.242 }} 2.060
add_atom 3 {{ -5.431, -3.833, -5.849 }} 2.030
add_atom 4 {{ -4.657, -3.249, -5.603 }} 2.030
add_atom 5 {{ -4.481, -2.779, -4.941 }} 2.030
add_atom 6 {{ -4.699, -1.894, -4.529 }} 1.620
add_atom 7 {{ -4.292, -1.157, -3.994 }} 1.290
add_atom 8 {{ -4.131, -0.512, -3.334 }} 1.060
add_atom 9 {{ -3.473, -0.111, -2.809 }} 1.160
add_atom 10 {{ -2.798, 0.260, -2.306 }} 1.250
add_atom 11 {{ -1.854, -0.011, -2.187 }} 1.180
add_atom 12 {{ -1.135, -0.087, -1.699 }} 1.010
add_atom 13 {{ -0.869, -0.078, -0.735 }} 0.790
add_atom 14 {{ -0.979, -0.007, 0.118 }} 0.770
add_atom 15 {{ -0.276, 0.130, 0.713 }} 1.120
mol delrep 0 $channel2
mol addrep $channel2
mol selection {{all}}
mol rename top {channel2}


set channel3 [mol new atoms 19]
mol top $channel3
animate dup $channel3
mol color ColorID 3
mol representation VDW 1 60
add_atom 0 {{ -7.568, -3.569, -5.216 }} 1.590
add_atom 1 {{ -7.037, -3.997, -5.948 }} 1.800
add_atom 2 {{ -6.198, -4.175, -6.242 }} 2.060
add_atom 3 {{ -5.431, -3.833, -5.849 }} 2.030
add_atom 4 {{ -4.657, -3.249, -5.603 }} 2.030
add_atom 5 {{ -4.371, -2.860, -4.953 }} 2.050
add_atom 6 {{ -3.407, -2.921, -4.787 }} 1.870
add_atom 7 {{ -2.625, -2.841, -4.279 }} 1.370
add_atom 8 {{ -1.893, -2.533, -3.670 }} 0.980
add_atom 9 {{ -1.162, -2.208, -3.070 }} 0.940
add_atom 10 {{ -0.669, -2.342, -2.415 }} 0.950
add_atom 11 {{ -0.764, -3.093, -1.822 }} 0.720
add_atom 12 {{ -1.023, -3.915, -1.316 }} 0.800
add_atom 13 {{ -1.373, -4.350, -0.649 }} 0.790
add_atom 14 {{ -1.872, -4.664, 0.051 }} 0.710
add_atom 15 {{ -2.523, -4.638, 0.755 }} 1.090
add_atom 16 {{ -3.199, -4.643, 1.390 }} 1.490
add_atom 17 {{ -3.630, -4.181, 2.146 }} 1.460
add_atom 18 {{ -4.054, -3.916, 2.980 }} 1.710
mol delrep 0 $channel3
mol addrep $channel3
mol selection {{all}}
mol rename top {channel3}

display reset view