from pymol import cmd from pymol.cgo import * import chempy def add_atom(model, name, vdw, x, y, z): a = chempy.Atom() a.name = name a.vdw = vdw a.coord = [x, y, z] model.atom.append(a) def channel1(): model = chempy.models.Indexed() add_atom(model, '0', 3.129, -4.146, 38.618, 59.435) add_atom(model, '1', 3.115, -4.118, 38.591, 59.358) add_atom(model, '2', 3.101, -4.090, 38.565, 59.281) add_atom(model, '3', 3.087, -4.064, 38.540, 59.203) add_atom(model, '4', 3.073, -4.038, 38.517, 59.125) add_atom(model, '5', 3.059, -4.015, 38.496, 59.046) add_atom(model, '6', 3.045, -3.994, 38.479, 58.967) add_atom(model, '7', 3.028, -3.975, 38.466, 58.887) add_atom(model, '8', 3.008, -3.960, 38.457, 58.805) add_atom(model, '9', 2.984, -3.948, 38.453, 58.723) add_atom(model, '10', 2.957, -3.940, 38.454, 58.639) add_atom(model, '11', 2.927, -3.935, 38.459, 58.558) add_atom(model, '12', 2.895, -3.933, 38.466, 58.481) add_atom(model, '13', 2.867, -3.934, 38.474, 58.410) add_atom(model, '14', 2.843, -3.936, 38.481, 58.349) add_atom(model, '15', 2.826, -3.940, 38.486, 58.300) add_atom(model, '16', 2.815, -3.944, 38.486, 58.265) add_atom(model, '17', 2.811, -3.949, 38.481, 58.247) add_atom(model, '18', 2.813, -3.954, 38.469, 58.247) add_atom(model, '19', 2.819, -3.957, 38.451, 58.265) add_atom(model, '20', 2.829, -3.959, 38.431, 58.291) add_atom(model, '21', 2.841, -3.958, 38.412, 58.317) add_atom(model, '22', 2.852, -3.953, 38.399, 58.333) add_atom(model, '23', 2.859, -3.944, 38.395, 58.333) add_atom(model, '24', 2.859, -3.928, 38.405, 58.305) add_atom(model, '25', 2.841, -3.905, 38.432, 58.244) add_atom(model, '26', 2.791, -3.874, 38.480, 58.138) add_atom(model, '27', 2.699, -3.835, 38.553, 57.982) add_atom(model, '28', 2.573, -3.788, 38.649, 57.777) add_atom(model, '29', 2.432, -3.735, 38.762, 57.537) add_atom(model, '30', 2.294, -3.680, 38.886, 57.272) add_atom(model, '31', 2.172, -3.623, 39.015, 56.993) add_atom(model, '32', 2.075, -3.569, 39.143, 56.712) add_atom(model, '33', 2.010, -3.519, 39.266, 56.440) add_atom(model, '34', 1.979, -3.476, 39.375, 56.190) add_atom(model, '35', 1.968, -3.441, 39.467, 55.972) add_atom(model, '36', 1.960, -3.418, 39.535, 55.795) add_atom(model, '37', 1.942, -3.405, 39.582, 55.660) add_atom(model, '38', 1.917, -3.399, 39.611, 55.562) add_atom(model, '39', 1.895, -3.399, 39.625, 55.495) add_atom(model, '40', 1.885, -3.402, 39.629, 55.456) add_atom(model, '41', 1.887, -3.406, 39.626, 55.439) add_atom(model, '42', 1.894, -3.409, 39.621, 55.440) add_atom(model, '43', 1.901, -3.409, 39.615, 55.454) add_atom(model, '44', 1.902, -3.403, 39.615, 55.476) add_atom(model, '45', 1.897, -3.391, 39.621, 55.503) add_atom(model, '46', 1.883, -3.376, 39.631, 55.528) add_atom(model, '47', 1.862, -3.359, 39.645, 55.546) add_atom(model, '48', 1.842, -3.346, 39.657, 55.554) add_atom(model, '49', 1.834, -3.338, 39.667, 55.546) add_atom(model, '50', 1.847, -3.340, 39.671, 55.516) add_atom(model, '51', 1.867, -3.355, 39.667, 55.461) add_atom(model, '52', 1.873, -3.385, 39.651, 55.374) add_atom(model, '53', 1.844, -3.435, 39.623, 55.252) add_atom(model, '54', 1.777, -3.504, 39.579, 55.094) add_atom(model, '55', 1.693, -3.589, 39.524, 54.906) add_atom(model, '56', 1.610, -3.683, 39.458, 54.697) add_atom(model, '57', 1.545, -3.783, 39.385, 54.474) add_atom(model, '58', 1.499, -3.882, 39.307, 54.245) add_atom(model, '59', 1.472, -3.977, 39.227, 54.019) add_atom(model, '60', 1.464, -4.061, 39.146, 53.802) add_atom(model, '61', 1.464, -4.130, 39.068, 53.603) add_atom(model, '62', 1.456, -4.180, 38.995, 53.429) add_atom(model, '63', 1.429, -4.208, 38.927, 53.284) add_atom(model, '64', 1.387, -4.218, 38.867, 53.165) add_atom(model, '65', 1.348, -4.213, 38.813, 53.072) add_atom(model, '66', 1.331, -4.195, 38.766, 53.002) add_atom(model, '67', 1.340, -4.168, 38.728, 52.955) add_atom(model, '68', 1.359, -4.134, 38.698, 52.927) add_atom(model, '69', 1.369, -4.096, 38.676, 52.918) add_atom(model, '70', 1.358, -4.058, 38.664, 52.927) add_atom(model, '71', 1.330, -4.021, 38.661, 52.950) add_atom(model, '72', 1.296, -3.988, 38.665, 52.981) add_atom(model, '73', 1.264, -3.959, 38.673, 53.011) add_atom(model, '74', 1.240, -3.936, 38.682, 53.029) add_atom(model, '75', 1.226, -3.919, 38.688, 53.026) add_atom(model, '76', 1.224, -3.909, 38.688, 52.993) add_atom(model, '77', 1.231, -3.907, 38.678, 52.919) add_atom(model, '78', 1.232, -3.915, 38.656, 52.796) add_atom(model, '79', 1.212, -3.933, 38.618, 52.613) add_atom(model, '80', 1.170, -3.962, 38.562, 52.365) add_atom(model, '81', 1.127, -4.000, 38.490, 52.062) add_atom(model, '82', 1.112, -4.043, 38.408, 51.722) add_atom(model, '83', 1.143, -4.091, 38.319, 51.360) add_atom(model, '84', 1.218, -4.140, 38.229, 50.992) add_atom(model, '85', 1.325, -4.187, 38.141, 50.636) add_atom(model, '86', 1.452, -4.231, 38.061, 50.307) add_atom(model, '87', 1.577, -4.268, 37.992, 50.021) add_atom(model, '88', 1.675, -4.296, 37.939, 49.795) add_atom(model, '89', 1.721, -4.314, 37.905, 49.639) add_atom(model, '90', 1.711, -4.323, 37.888, 49.544) add_atom(model, '91', 1.677, -4.325, 37.884, 49.500) add_atom(model, '92', 1.653, -4.321, 37.892, 49.496) add_atom(model, '93', 1.661, -4.313, 37.907, 49.523) add_atom(model, '94', 1.687, -4.304, 37.929, 49.569) add_atom(model, '95', 1.709, -4.294, 37.952, 49.625) add_atom(model, '96', 1.711, -4.286, 37.976, 49.680) add_atom(model, '97', 1.694, -4.281, 37.997, 49.724) add_atom(model, '98', 1.672, -4.281, 38.015, 49.750) add_atom(model, '99', 1.657, -4.287, 38.030, 49.760) add_atom(model, '100', 1.652, -4.300, 38.046, 49.753) add_atom(model, '101', 1.651, -4.322, 38.064, 49.731) add_atom(model, '102', 1.650, -4.353, 38.087, 49.695) add_atom(model, '103', 1.641, -4.395, 38.116, 49.644) add_atom(model, '104', 1.621, -4.450, 38.154, 49.581) add_atom(model, '105', 1.582, -4.517, 38.203, 49.505) add_atom(model, '106', 1.523, -4.600, 38.264, 49.417) add_atom(model, '107', 1.451, -4.695, 38.336, 49.318) add_atom(model, '108', 1.378, -4.801, 38.414, 49.210) add_atom(model, '109', 1.315, -4.915, 38.493, 49.093) add_atom(model, '110', 1.269, -5.033, 38.568, 48.968) add_atom(model, '111', 1.246, -5.154, 38.634, 48.837) add_atom(model, '112', 1.251, -5.273, 38.687, 48.700) add_atom(model, '113', 1.277, -5.389, 38.721, 48.559) add_atom(model, '114', 1.301, -5.498, 38.731, 48.414) add_atom(model, '115', 1.302, -5.598, 38.715, 48.267) add_atom(model, '116', 1.266, -5.688, 38.673, 48.118) add_atom(model, '117', 1.215, -5.770, 38.611, 47.970) add_atom(model, '118', 1.176, -5.843, 38.535, 47.824) add_atom(model, '119', 1.174, -5.908, 38.449, 47.682) add_atom(model, '120', 1.201, -5.965, 38.358, 47.544) add_atom(model, '121', 1.239, -6.016, 38.269, 47.412) add_atom(model, '122', 1.269, -6.060, 38.185, 47.289) add_atom(model, '123', 1.286, -6.099, 38.112, 47.174) add_atom(model, '124', 1.292, -6.132, 38.054, 47.069) add_atom(model, '125', 1.293, -6.160, 38.010, 46.973) add_atom(model, '126', 1.293, -6.184, 37.978, 46.884) add_atom(model, '127', 1.296, -6.203, 37.956, 46.799) add_atom(model, '128', 1.306, -6.217, 37.943, 46.717) add_atom(model, '129', 1.328, -6.227, 37.935, 46.635) add_atom(model, '130', 1.354, -6.233, 37.932, 46.552) add_atom(model, '131', 1.379, -6.235, 37.931, 46.466) add_atom(model, '132', 1.395, -6.233, 37.931, 46.374) add_atom(model, '133', 1.404, -6.228, 37.930, 46.276) add_atom(model, '134', 1.410, -6.220, 37.928, 46.173) add_atom(model, '135', 1.416, -6.208, 37.928, 46.065) add_atom(model, '136', 1.426, -6.193, 37.930, 45.955) add_atom(model, '137', 1.437, -6.176, 37.934, 45.842) add_atom(model, '138', 1.449, -6.155, 37.942, 45.729) add_atom(model, '139', 1.460, -6.132, 37.955, 45.616) add_atom(model, '140', 1.470, -6.107, 37.973, 45.505) add_atom(model, '141', 1.476, -6.080, 37.998, 45.396) add_atom(model, '142', 1.479, -6.050, 38.029, 45.291) add_atom(model, '143', 1.479, -6.016, 38.064, 45.190) add_atom(model, '144', 1.479, -5.979, 38.103, 45.093) add_atom(model, '145', 1.481, -5.937, 38.143, 45.002) add_atom(model, '146', 1.485, -5.890, 38.183, 44.915) add_atom(model, '147', 1.491, -5.836, 38.221, 44.835) add_atom(model, '148', 1.497, -5.775, 38.257, 44.761) add_atom(model, '149', 1.503, -5.707, 38.287, 44.693) add_atom(model, '150', 1.510, -5.631, 38.312, 44.633) add_atom(model, '151', 1.520, -5.547, 38.329, 44.577) add_atom(model, '152', 1.532, -5.459, 38.339, 44.520) add_atom(model, '153', 1.548, -5.369, 38.340, 44.459) add_atom(model, '154', 1.565, -5.279, 38.332, 44.387) add_atom(model, '155', 1.585, -5.191, 38.315, 44.301) add_atom(model, '156', 1.601, -5.108, 38.289, 44.196) add_atom(model, '157', 1.608, -5.032, 38.251, 44.068) add_atom(model, '158', 1.600, -4.965, 38.203, 43.911) add_atom(model, '159', 1.578, -4.910, 38.143, 43.722) add_atom(model, '160', 1.552, -4.866, 38.074, 43.508) add_atom(model, '161', 1.536, -4.831, 38.000, 43.278) add_atom(model, '162', 1.537, -4.804, 37.922, 43.040) add_atom(model, '163', 1.553, -4.784, 37.845, 42.803) add_atom(model, '164', 1.582, -4.769, 37.772, 42.577) add_atom(model, '165', 1.619, -4.758, 37.705, 42.371) add_atom(model, '166', 1.657, -4.750, 37.648, 42.193) add_atom(model, '167', 1.684, -4.742, 37.603, 42.052) add_atom(model, '168', 1.691, -4.734, 37.574, 41.954) add_atom(model, '169', 1.681, -4.728, 37.557, 41.894) add_atom(model, '170', 1.666, -4.723, 37.550, 41.862) add_atom(model, '171', 1.659, -4.721, 37.553, 41.853) add_atom(model, '172', 1.665, -4.724, 37.561, 41.857) add_atom(model, '173', 1.677, -4.732, 37.573, 41.868) add_atom(model, '174', 1.687, -4.746, 37.586, 41.878) add_atom(model, '175', 1.687, -4.767, 37.598, 41.879) add_atom(model, '176', 1.676, -4.797, 37.607, 41.863) add_atom(model, '177', 1.658, -4.836, 37.612, 41.827) add_atom(model, '178', 1.632, -4.880, 37.616, 41.772) add_atom(model, '179', 1.604, -4.928, 37.621, 41.700) add_atom(model, '180', 1.578, -4.977, 37.629, 41.613) add_atom(model, '181', 1.559, -5.026, 37.642, 41.514) add_atom(model, '182', 1.548, -5.071, 37.664, 41.405) add_atom(model, '183', 1.541, -5.109, 37.696, 41.287) add_atom(model, '184', 1.534, -5.140, 37.741, 41.164) add_atom(model, '185', 1.525, -5.160, 37.801, 41.037) add_atom(model, '186', 1.516, -5.170, 37.876, 40.907) add_atom(model, '187', 1.510, -5.172, 37.959, 40.775) add_atom(model, '188', 1.509, -5.168, 38.045, 40.641) add_atom(model, '189', 1.518, -5.162, 38.131, 40.507) add_atom(model, '190', 1.544, -5.155, 38.210, 40.372) add_atom(model, '191', 1.589, -5.151, 38.278, 40.236) add_atom(model, '192', 1.643, -5.151, 38.330, 40.102) add_atom(model, '193', 1.684, -5.158, 38.361, 39.968) add_atom(model, '194', 1.688, -5.175, 38.366, 39.835) add_atom(model, '195', 1.651, -5.200, 38.348, 39.706) add_atom(model, '196', 1.595, -5.230, 38.311, 39.580) add_atom(model, '197', 1.546, -5.262, 38.260, 39.459) add_atom(model, '198', 1.522, -5.293, 38.201, 39.345) add_atom(model, '199', 1.518, -5.320, 38.138, 39.239) add_atom(model, '200', 1.522, -5.340, 38.076, 39.142) add_atom(model, '201', 1.522, -5.350, 38.021, 39.056) add_atom(model, '202', 1.519, -5.348, 37.977, 38.981) add_atom(model, '203', 1.515, -5.330, 37.948, 38.919) add_atom(model, '204', 1.516, -5.301, 37.934, 38.867) add_atom(model, '205', 1.525, -5.263, 37.935, 38.820) add_atom(model, '206', 1.544, -5.220, 37.948, 38.776) add_atom(model, '207', 1.574, -5.177, 37.972, 38.731) add_atom(model, '208', 1.615, -5.138, 38.007, 38.680) add_atom(model, '209', 1.654, -5.105, 38.050, 38.621) add_atom(model, '210', 1.681, -5.084, 38.102, 38.549) add_atom(model, '211', 1.684, -5.078, 38.159, 38.461) add_atom(model, '212', 1.668, -5.088, 38.221, 38.355) add_atom(model, '213', 1.640, -5.112, 38.283, 38.233) add_atom(model, '214', 1.608, -5.146, 38.342, 38.096) add_atom(model, '215', 1.582, -5.187, 38.393, 37.947) add_atom(model, '216', 1.574, -5.230, 38.433, 37.789) add_atom(model, '217', 1.595, -5.271, 38.457, 37.623) add_atom(model, '218', 1.643, -5.308, 38.461, 37.451) add_atom(model, '219', 1.696, -5.336, 38.442, 37.277) add_atom(model, '220', 1.730, -5.352, 38.395, 37.101) add_atom(model, '221', 1.729, -5.355, 38.321, 36.926) add_atom(model, '222', 1.704, -5.347, 38.226, 36.755) add_atom(model, '223', 1.675, -5.331, 38.116, 36.591) add_atom(model, '224', 1.657, -5.309, 37.998, 36.434) add_atom(model, '225', 1.653, -5.285, 37.878, 36.289) add_atom(model, '226', 1.658, -5.261, 37.761, 36.157) add_atom(model, '227', 1.669, -5.240, 37.656, 36.040) add_atom(model, '228', 1.682, -5.224, 37.567, 35.942) add_atom(model, '229', 1.694, -5.217, 37.501, 35.864) add_atom(model, '230', 1.704, -5.217, 37.459, 35.806) add_atom(model, '231', 1.710, -5.225, 37.437, 35.766) add_atom(model, '232', 1.713, -5.237, 37.431, 35.740) add_atom(model, '233', 1.713, -5.254, 37.439, 35.728) add_atom(model, '234', 1.711, -5.273, 37.456, 35.726) add_atom(model, '235', 1.708, -5.293, 37.479, 35.732) add_atom(model, '236', 1.704, -5.311, 37.505, 35.743) add_atom(model, '237', 1.700, -5.328, 37.531, 35.758) add_atom(model, '238', 1.698, -5.341, 37.553, 35.774) add_atom(model, '239', 1.696, -5.350, 37.570, 35.788) add_atom(model, '240', 1.696, -5.356, 37.582, 35.799) add_atom(model, '241', 1.698, -5.358, 37.590, 35.806) add_atom(model, '242', 1.701, -5.358, 37.592, 35.805) add_atom(model, '243', 1.702, -5.354, 37.590, 35.796) add_atom(model, '244', 1.700, -5.349, 37.582, 35.776) add_atom(model, '245', 1.693, -5.341, 37.570, 35.744) add_atom(model, '246', 1.676, -5.331, 37.552, 35.697) add_atom(model, '247', 1.645, -5.319, 37.529, 35.635) add_atom(model, '248', 1.604, -5.306, 37.502, 35.559) add_atom(model, '249', 1.556, -5.292, 37.472, 35.472) add_atom(model, '250', 1.507, -5.277, 37.438, 35.377) add_atom(model, '251', 1.458, -5.263, 37.403, 35.275) add_atom(model, '252', 1.412, -5.249, 37.366, 35.169) add_atom(model, '253', 1.368, -5.235, 37.329, 35.061) add_atom(model, '254', 1.327, -5.223, 37.292, 34.954) add_atom(model, '255', 1.291, -5.212, 37.256, 34.851) add_atom(model, '256', 1.259, -5.203, 37.222, 34.752) add_atom(model, '257', 1.231, -5.193, 37.190, 34.654) add_atom(model, '258', 1.207, -5.180, 37.159, 34.555) add_atom(model, '259', 1.184, -5.164, 37.130, 34.452) add_atom(model, '260', 1.162, -5.142, 37.103, 34.343) add_atom(model, '261', 1.137, -5.112, 37.077, 34.225) add_atom(model, '262', 1.108, -5.072, 37.053, 34.095) add_atom(model, '263', 1.074, -5.022, 37.031, 33.950) add_atom(model, '264', 1.035, -4.958, 37.010, 33.788) add_atom(model, '265', 1.001, -4.883, 36.991, 33.609) add_atom(model, '266', 0.978, -4.799, 36.974, 33.418) add_atom(model, '267', 0.974, -4.713, 36.959, 33.219) add_atom(model, '268', 0.992, -4.626, 36.948, 33.015) add_atom(model, '269', 1.033, -4.545, 36.941, 32.811) add_atom(model, '270', 1.099, -4.473, 36.937, 32.611) add_atom(model, '271', 1.176, -4.413, 36.937, 32.420) add_atom(model, '272', 1.244, -4.371, 36.942, 32.240) add_atom(model, '273', 1.286, -4.350, 36.952, 32.077) add_atom(model, '274', 1.304, -4.350, 36.965, 31.929) add_atom(model, '275', 1.320, -4.369, 36.977, 31.794) add_atom(model, '276', 1.356, -4.405, 36.987, 31.667) add_atom(model, '277', 1.423, -4.454, 36.989, 31.545) add_atom(model, '278', 1.513, -4.515, 36.983, 31.426) add_atom(model, '279', 1.612, -4.586, 36.963, 31.306) add_atom(model, '280', 1.710, -4.663, 36.927, 31.182) add_atom(model, '281', 1.801, -4.745, 36.872, 31.050) add_atom(model, '282', 1.882, -4.829, 36.796, 30.908) add_atom(model, '283', 1.951, -4.912, 36.705, 30.753) add_atom(model, '284', 2.019, -4.988, 36.609, 30.584) add_atom(model, '285', 2.110, -5.055, 36.516, 30.401) add_atom(model, '286', 2.245, -5.107, 36.434, 30.201) add_atom(model, '287', 2.425, -5.141, 36.372, 29.984) add_atom(model, '288', 2.622, -5.152, 36.339, 29.748) add_atom(model, '289', 2.806, -5.137, 36.344, 29.491) add_atom(model, '290', 2.958, -5.090, 36.396, 29.214) add_atom(model, '291', 3.092, -5.012, 36.498, 28.916) add_atom(model, '292', 3.227, -4.907, 36.641, 28.605) add_atom(model, '293', 3.382, -4.783, 36.814, 28.291) add_atom(model, '294', 3.555, -4.647, 37.006, 27.983) add_atom(model, '295', 3.741, -4.507, 37.206, 27.688) add_atom(model, '296', 3.933, -4.370, 37.401, 27.417) add_atom(model, '297', 4.119, -4.242, 37.582, 27.178) add_atom(model, '298', 4.282, -4.133, 37.736, 26.979) add_atom(model, '299', 4.406, -4.047, 37.852, 26.830) add_atom(model, '300', 4.483, -3.989, 37.927, 26.733) add_atom(model, '301', 4.523, -3.954, 37.965, 26.677) add_atom(model, '302', 4.536, -3.937, 37.973, 26.653) add_atom(model, '303', 4.532, -3.934, 37.957, 26.650) add_atom(model, '304', 4.521, -3.940, 37.924, 26.659) add_atom(model, '305', 4.511, -3.950, 37.879, 26.669) add_atom(model, '306', 4.512, -3.960, 37.829, 26.670) add_atom(model, '307', 4.527, -3.965, 37.780, 26.652) add_atom(model, '308', 4.557, -3.960, 37.738, 26.605) add_atom(model, '309', 4.603, -3.945, 37.705, 26.528) add_atom(model, '310', 4.664, -3.921, 37.680, 26.428) add_atom(model, '311', 4.737, -3.891, 37.661, 26.311) add_atom(model, '312', 4.817, -3.857, 37.647, 26.182) add_atom(model, '313', 4.900, -3.819, 37.635, 26.049) add_atom(model, '314', 4.983, -3.782, 37.626, 25.918) add_atom(model, '315', 5.061, -3.745, 37.616, 25.795) add_atom(model, '316', 5.131, -3.712, 37.604, 25.687) add_atom(model, '317', 5.190, -3.685, 37.590, 25.598) add_atom(model, '318', 5.238, -3.663, 37.572, 25.530) add_atom(model, '319', 5.274, -3.645, 37.552, 25.480) add_atom(model, '320', 5.298, -3.631, 37.530, 25.445) add_atom(model, '321', 5.313, -3.621, 37.505, 25.422) add_atom(model, '322', 5.321, -3.614, 37.479, 25.410) add_atom(model, '323', 5.324, -3.608, 37.452, 25.406) add_atom(model, '324', 5.324, -3.604, 37.423, 25.406) add_atom(model, '325', 5.322, -3.601, 37.395, 25.409) for a in range(len(model.atom) - 1): b = chempy.Bond() b.index = [a, a + 1] model.bond.append(b) cmd.set('surface_mode', 1) cmd.set('sphere_mode', 9) cmd.set('mesh_mode', 1) cmd.load_model(model, 'channel1') cmd.hide('everything', 'channel1') cmd.set('sphere_color', 'red', 'channel1') cmd.show('spheres', 'channel1') channel1() cmd.group('Channels', [channel1], 'add') def channel2(): model = chempy.models.Indexed() add_atom(model, '0', 1.900, -5.031, 37.103, 57.141) add_atom(model, '1', 2.240, -4.567, 37.515, 57.778) for a in range(len(model.atom) - 1): b = chempy.Bond() b.index = [a, a + 1] model.bond.append(b) cmd.set('surface_mode', 1) cmd.set('sphere_mode', 9) cmd.set('mesh_mode', 1) cmd.load_model(model, 'channel2') cmd.hide('everything', 'channel2') cmd.set('sphere_color', 'green', 'channel2') cmd.show('spheres', 'channel2') channel2() cmd.group('Channels', [channel2], 'add') def channel3(): model = chempy.models.Indexed() add_atom(model, '0', 1.900, -5.031, 37.103, 57.141) add_atom(model, '1', 2.230, -4.523, 37.577, 57.658) add_atom(model, '2', 2.700, -3.956, 38.312, 58.030) add_atom(model, '3', 2.330, -3.819, 38.753, 57.298) add_atom(model, '4', 2.010, -3.626, 39.172, 56.410) add_atom(model, '5', 1.950, -3.441, 39.525, 55.656) add_atom(model, '6', 1.610, -3.739, 39.358, 54.749) add_atom(model, '7', 1.450, -4.102, 39.065, 53.864) add_atom(model, '8', 1.420, -4.246, 38.653, 53.023) add_atom(model, '9', 1.010, -3.854, 38.754, 52.170) add_atom(model, '10', 1.150, -3.951, 38.350, 51.370) add_atom(model, '11', 1.400, -4.190, 38.101, 50.450) add_atom(model, '12', 1.660, -4.439, 38.066, 49.531) add_atom(model, '13', 1.390, -5.069, 38.396, 48.827) add_atom(model, '14', 1.310, -5.610, 38.449, 48.082) add_atom(model, '15', 1.330, -5.999, 38.023, 47.265) add_atom(model, '16', 1.420, -6.147, 37.693, 46.455) add_atom(model, '17', 1.490, -6.034, 37.863, 45.516) add_atom(model, '18', 1.510, -5.585, 38.189, 44.684) add_atom(model, '19', 1.610, -4.912, 38.103, 43.955) add_atom(model, '20', 1.560, -4.747, 37.825, 43.033) add_atom(model, '21', 1.650, -4.730, 37.610, 42.073) add_atom(model, '22', 1.550, -5.039, 37.652, 41.232) add_atom(model, '23', 1.610, -5.038, 38.128, 40.354) add_atom(model, '24', 1.620, -5.120, 38.180, 39.454) add_atom(model, '25', 1.710, -4.978, 38.155, 38.588) add_atom(model, '26', 1.660, -5.152, 38.346, 37.631) add_atom(model, '27', 1.660, -5.421, 38.316, 36.736) add_atom(model, '28', 1.660, -5.434, 37.841, 35.931) add_atom(model, '29', 1.490, -5.166, 37.319, 35.343) add_atom(model, '30', 1.130, -5.108, 37.072, 34.376) add_atom(model, '31', 0.960, -5.012, 37.012, 33.597) add_atom(model, '32', 1.040, -5.396, 36.939, 32.725) for a in range(len(model.atom) - 1): b = chempy.Bond() b.index = [a, a + 1] model.bond.append(b) cmd.set('surface_mode', 1) cmd.set('sphere_mode', 9) cmd.set('mesh_mode', 1) cmd.load_model(model, 'channel3') cmd.hide('everything', 'channel3') cmd.set('sphere_color', 'blue', 'channel3') cmd.show('spheres', 'channel3') channel3() cmd.group('Channels', [channel3], 'add') def channel4(): model = chempy.models.Indexed() add_atom(model, '0', 5.211, -6.396, 35.791, 21.987) add_atom(model, '1', 5.067, -6.693, 35.788, 22.070) add_atom(model, '2', 4.928, -6.979, 35.786, 22.155) add_atom(model, '3', 4.801, -7.242, 35.786, 22.243) add_atom(model, '4', 4.691, -7.471, 35.791, 22.335) add_atom(model, '5', 4.605, -7.653, 35.801, 22.433) add_atom(model, '6', 4.540, -7.779, 35.818, 22.538) add_atom(model, '7', 4.488, -7.835, 35.842, 22.652) add_atom(model, '8', 4.443, -7.811, 35.876, 22.776) add_atom(model, '9', 4.396, -7.695, 35.920, 22.911) add_atom(model, '10', 4.347, -7.477, 35.977, 23.060) add_atom(model, '11', 4.318, -7.159, 36.045, 23.221) add_atom(model, '12', 4.332, -6.762, 36.123, 23.391) add_atom(model, '13', 4.414, -6.310, 36.209, 23.568) add_atom(model, '14', 4.586, -5.822, 36.301, 23.749) add_atom(model, '15', 4.824, -5.322, 36.397, 23.931) add_atom(model, '16', 5.078, -4.831, 36.495, 24.110) add_atom(model, '17', 5.294, -4.371, 36.593, 24.283) add_atom(model, '18', 5.422, -3.964, 36.689, 24.449) add_atom(model, '19', 5.437, -3.632, 36.782, 24.603) add_atom(model, '20', 5.376, -3.392, 36.869, 24.743) add_atom(model, '21', 5.282, -3.241, 36.950, 24.869) add_atom(model, '22', 5.198, -3.164, 37.025, 24.981) add_atom(model, '23', 5.163, -3.149, 37.095, 25.080) add_atom(model, '24', 5.175, -3.183, 37.160, 25.166) add_atom(model, '25', 5.212, -3.253, 37.219, 25.239) add_atom(model, '26', 5.255, -3.344, 37.273, 25.300) add_atom(model, '27', 5.280, -3.445, 37.322, 25.350) add_atom(model, '28', 5.281, -3.542, 37.367, 25.389) add_atom(model, '29', 5.263, -3.622, 37.406, 25.416) add_atom(model, '30', 5.238, -3.678, 37.442, 25.435) add_atom(model, '31', 5.216, -3.713, 37.473, 25.447) add_atom(model, '32', 5.203, -3.731, 37.500, 25.457) add_atom(model, '33', 5.200, -3.736, 37.524, 25.467) add_atom(model, '34', 5.200, -3.732, 37.544, 25.482) add_atom(model, '35', 5.199, -3.722, 37.562, 25.503) add_atom(model, '36', 5.191, -3.712, 37.576, 25.536) add_atom(model, '37', 5.174, -3.705, 37.589, 25.582) add_atom(model, '38', 5.146, -3.704, 37.599, 25.646) add_atom(model, '39', 5.107, -3.715, 37.608, 25.730) add_atom(model, '40', 5.055, -3.735, 37.615, 25.831) add_atom(model, '41', 4.992, -3.763, 37.623, 25.945) add_atom(model, '42', 4.920, -3.796, 37.632, 26.066) add_atom(model, '43', 4.844, -3.832, 37.643, 26.188) add_atom(model, '44', 4.767, -3.868, 37.658, 26.307) add_atom(model, '45', 4.693, -3.902, 37.676, 26.418) add_atom(model, '46', 4.628, -3.931, 37.700, 26.514) add_atom(model, '47', 4.573, -3.953, 37.730, 26.591) add_atom(model, '48', 4.532, -3.965, 37.767, 26.643) add_atom(model, '49', 4.508, -3.967, 37.812, 26.668) add_atom(model, '50', 4.502, -3.962, 37.858, 26.674) add_atom(model, '51', 4.509, -3.953, 37.903, 26.668) add_atom(model, '52', 4.521, -3.945, 37.940, 26.658) add_atom(model, '53', 4.532, -3.941, 37.966, 26.652) add_atom(model, '54', 4.535, -3.946, 37.975, 26.659) add_atom(model, '55', 4.522, -3.962, 37.962, 26.685) add_atom(model, '56', 4.484, -3.995, 37.923, 26.739) add_atom(model, '57', 4.412, -4.047, 37.853, 26.830) add_atom(model, '58', 4.298, -4.123, 37.748, 26.963) add_atom(model, '59', 4.141, -4.221, 37.610, 27.140) add_atom(model, '60', 3.960, -4.334, 37.448, 27.352) add_atom(model, '61', 3.777, -4.458, 37.272, 27.594) add_atom(model, '62', 3.611, -4.587, 37.089, 27.857) add_atom(model, '63', 3.481, -4.714, 36.908, 28.136) add_atom(model, '64', 3.378, -4.835, 36.738, 28.423) add_atom(model, '65', 3.281, -4.944, 36.589, 28.711) add_atom(model, '66', 3.170, -5.034, 36.467, 28.994) add_atom(model, '67', 3.024, -5.101, 36.383, 29.264) add_atom(model, '68', 2.838, -5.140, 36.342, 29.516) add_atom(model, '69', 2.633, -5.153, 36.340, 29.751) add_atom(model, '70', 2.433, -5.143, 36.369, 29.968) add_atom(model, '71', 2.261, -5.114, 36.423, 30.169) add_atom(model, '72', 2.135, -5.069, 36.495, 30.356) add_atom(model, '73', 2.047, -5.011, 36.579, 30.528) add_atom(model, '74', 1.982, -4.944, 36.667, 30.688) add_atom(model, '75', 1.923, -4.870, 36.754, 30.835) add_atom(model, '76', 1.855, -4.792, 36.832, 30.972) add_atom(model, '77', 1.771, -4.715, 36.894, 31.098) add_atom(model, '78', 1.679, -4.641, 36.939, 31.217) add_atom(model, '79', 1.588, -4.571, 36.968, 31.330) add_atom(model, '80', 1.505, -4.508, 36.984, 31.440) add_atom(model, '81', 1.436, -4.452, 36.989, 31.549) add_atom(model, '82', 1.379, -4.407, 36.987, 31.660) add_atom(model, '83', 1.331, -4.373, 36.979, 31.776) add_atom(model, '84', 1.286, -4.353, 36.968, 31.899) add_atom(model, '85', 1.243, -4.348, 36.955, 32.032) add_atom(model, '86', 1.198, -4.361, 36.945, 32.177) add_atom(model, '87', 1.154, -4.392, 36.939, 32.336) add_atom(model, '88', 1.111, -4.439, 36.936, 32.506) add_atom(model, '89', 1.071, -4.499, 36.938, 32.686) add_atom(model, '90', 1.035, -4.568, 36.942, 32.871) add_atom(model, '91', 1.006, -4.645, 36.950, 33.059) add_atom(model, '92', 0.987, -4.724, 36.961, 33.245) add_atom(model, '93', 0.982, -4.804, 36.975, 33.428) add_atom(model, '94', 0.994, -4.880, 36.990, 33.603) add_atom(model, '95', 1.019, -4.950, 37.007, 33.768) add_atom(model, '96', 1.053, -5.010, 37.026, 33.920) add_atom(model, '97', 1.090, -5.060, 37.047, 34.056) add_atom(model, '98', 1.124, -5.099, 37.068, 34.180) add_atom(model, '99', 1.151, -5.130, 37.091, 34.292) add_atom(model, '100', 1.173, -5.153, 37.116, 34.396) add_atom(model, '101', 1.193, -5.171, 37.142, 34.494) add_atom(model, '102', 1.214, -5.185, 37.169, 34.586) add_atom(model, '103', 1.237, -5.195, 37.197, 34.677) add_atom(model, '104', 1.264, -5.204, 37.227, 34.767) add_atom(model, '105', 1.294, -5.213, 37.259, 34.858) add_atom(model, '106', 1.327, -5.223, 37.292, 34.953) add_atom(model, '107', 1.364, -5.234, 37.325, 35.051) add_atom(model, '108', 1.404, -5.246, 37.360, 35.150) add_atom(model, '109', 1.446, -5.259, 37.393, 35.248) add_atom(model, '110', 1.490, -5.273, 37.426, 35.343) add_atom(model, '111', 1.535, -5.286, 37.458, 35.433) add_atom(model, '112', 1.580, -5.299, 37.487, 35.517) add_atom(model, '113', 1.622, -5.311, 37.514, 35.592) add_atom(model, '114', 1.658, -5.323, 37.538, 35.658) add_atom(model, '115', 1.686, -5.333, 37.557, 35.710) add_atom(model, '116', 1.703, -5.342, 37.572, 35.750) add_atom(model, '117', 1.708, -5.349, 37.583, 35.778) add_atom(model, '118', 1.705, -5.355, 37.590, 35.796) add_atom(model, '119', 1.699, -5.358, 37.592, 35.805) add_atom(model, '120', 1.694, -5.359, 37.590, 35.806) add_atom(model, '121', 1.693, -5.357, 37.584, 35.801) add_atom(model, '122', 1.695, -5.353, 37.574, 35.792) add_atom(model, '123', 1.699, -5.345, 37.560, 35.780) add_atom(model, '124', 1.704, -5.335, 37.542, 35.766) add_atom(model, '125', 1.708, -5.321, 37.520, 35.751) add_atom(model, '126', 1.711, -5.305, 37.496, 35.739) add_atom(model, '127', 1.713, -5.287, 37.472, 35.730) add_atom(model, '128', 1.714, -5.269, 37.452, 35.726) add_atom(model, '129', 1.714, -5.252, 37.437, 35.729) add_atom(model, '130', 1.713, -5.237, 37.431, 35.741) add_atom(model, '131', 1.710, -5.225, 37.436, 35.764) add_atom(model, '132', 1.705, -5.218, 37.455, 35.800) add_atom(model, '133', 1.696, -5.216, 37.490, 35.850) add_atom(model, '134', 1.684, -5.221, 37.545, 35.917) add_atom(model, '135', 1.670, -5.233, 37.620, 36.001) add_atom(model, '136', 1.658, -5.251, 37.711, 36.101) add_atom(model, '137', 1.654, -5.272, 37.813, 36.215) add_atom(model, '138', 1.660, -5.294, 37.922, 36.342) add_atom(model, '139', 1.677, -5.316, 38.033, 36.479) add_atom(model, '140', 1.697, -5.335, 38.140, 36.625) add_atom(model, '141', 1.713, -5.348, 38.239, 36.777) add_atom(model, '142', 1.716, -5.355, 38.325, 36.935) add_atom(model, '143', 1.698, -5.353, 38.393, 37.095) add_atom(model, '144', 1.666, -5.339, 38.438, 37.256) add_atom(model, '145', 1.628, -5.315, 38.459, 37.417) add_atom(model, '146', 1.597, -5.282, 38.460, 37.576) add_atom(model, '147', 1.582, -5.245, 38.443, 37.730) add_atom(model, '148', 1.587, -5.206, 38.412, 37.878) add_atom(model, '149', 1.606, -5.167, 38.370, 38.020) add_atom(model, '150', 1.630, -5.132, 38.319, 38.152) add_atom(model, '151', 1.651, -5.103, 38.264, 38.273) add_atom(model, '152', 1.663, -5.084, 38.206, 38.381) add_atom(model, '153', 1.665, -5.078, 38.150, 38.475) add_atom(model, '154', 1.657, -5.085, 38.098, 38.554) add_atom(model, '155', 1.640, -5.105, 38.051, 38.620) add_atom(model, '156', 1.616, -5.134, 38.011, 38.675) add_atom(model, '157', 1.588, -5.170, 37.978, 38.722) add_atom(model, '158', 1.559, -5.209, 37.953, 38.765) add_atom(model, '159', 1.533, -5.249, 37.938, 38.805) add_atom(model, '160', 1.514, -5.286, 37.933, 38.847) add_atom(model, '161', 1.506, -5.317, 37.939, 38.892) add_atom(model, '162', 1.507, -5.339, 37.958, 38.944) add_atom(model, '163', 1.512, -5.350, 37.990, 39.005) add_atom(model, '164', 1.520, -5.349, 38.034, 39.077) add_atom(model, '165', 1.527, -5.337, 38.086, 39.158) add_atom(model, '166', 1.533, -5.318, 38.143, 39.248) add_atom(model, '167', 1.541, -5.293, 38.201, 39.346) add_atom(model, '168', 1.553, -5.264, 38.256, 39.450) add_atom(model, '169', 1.571, -5.235, 38.304, 39.561) add_atom(model, '170', 1.596, -5.207, 38.341, 39.675) add_atom(model, '171', 1.623, -5.182, 38.363, 39.793) add_atom(model, '172', 1.642, -5.164, 38.366, 39.914) add_atom(model, '173', 1.648, -5.153, 38.348, 40.037) add_atom(model, '174', 1.634, -5.150, 38.310, 40.160) add_atom(model, '175', 1.604, -5.152, 38.256, 40.284) add_atom(model, '176', 1.566, -5.157, 38.190, 40.408) add_atom(model, '177', 1.531, -5.163, 38.115, 40.532) add_atom(model, '178', 1.507, -5.169, 38.036, 40.656) add_atom(model, '179', 1.501, -5.172, 37.956, 40.778) add_atom(model, '180', 1.507, -5.170, 37.880, 40.899) add_atom(model, '181', 1.519, -5.162, 37.811, 41.019) add_atom(model, '182', 1.533, -5.145, 37.753, 41.136) add_atom(model, '183', 1.543, -5.120, 37.708, 41.251) add_atom(model, '184', 1.549, -5.086, 37.675, 41.361) add_atom(model, '185', 1.556, -5.047, 37.651, 41.465) add_atom(model, '186', 1.568, -5.004, 37.635, 41.560) add_atom(model, '187', 1.588, -4.959, 37.625, 41.647) add_atom(model, '188', 1.616, -4.914, 37.619, 41.722) add_atom(model, '189', 1.646, -4.870, 37.615, 41.785) add_atom(model, '190', 1.673, -4.830, 37.612, 41.832) add_atom(model, '191', 1.691, -4.796, 37.607, 41.864) add_atom(model, '192', 1.695, -4.768, 37.599, 41.879) add_atom(model, '193', 1.689, -4.748, 37.587, 41.879) add_atom(model, '194', 1.678, -4.734, 37.575, 41.871) add_atom(model, '195', 1.668, -4.725, 37.564, 41.860) add_atom(model, '196', 1.666, -4.722, 37.555, 41.853) add_atom(model, '197', 1.673, -4.722, 37.551, 41.856) add_atom(model, '198', 1.682, -4.725, 37.552, 41.874) add_atom(model, '199', 1.687, -4.730, 37.562, 41.913) add_atom(model, '200', 1.683, -4.737, 37.581, 41.980) add_atom(model, '201', 1.664, -4.744, 37.612, 42.080) add_atom(model, '202', 1.637, -4.751, 37.655, 42.216) add_atom(model, '203', 1.606, -4.759, 37.709, 42.383) add_atom(model, '204', 1.578, -4.769, 37.771, 42.573) add_atom(model, '205', 1.559, -4.783, 37.838, 42.780) add_atom(model, '206', 1.550, -4.800, 37.908, 42.997) add_atom(model, '207', 1.550, -4.823, 37.979, 43.216) add_atom(model, '208', 1.555, -4.853, 38.049, 43.430) add_atom(model, '209', 1.563, -4.890, 38.114, 43.634) add_atom(model, '210', 1.572, -4.936, 38.174, 43.819) add_atom(model, '211', 1.580, -4.991, 38.224, 43.979) add_atom(model, '212', 1.585, -5.056, 38.265, 44.113) add_atom(model, '213', 1.586, -5.128, 38.296, 44.224) add_atom(model, '214', 1.580, -5.205, 38.319, 44.317) add_atom(model, '215', 1.568, -5.286, 38.333, 44.394) add_atom(model, '216', 1.552, -5.369, 38.340, 44.459) add_atom(model, '217', 1.536, -5.452, 38.339, 44.516) add_atom(model, '218', 1.522, -5.533, 38.331, 44.568) add_atom(model, '219', 1.511, -5.611, 38.317, 44.619) add_atom(model, '220', 1.503, -5.683, 38.296, 44.673) add_atom(model, '221', 1.497, -5.749, 38.270, 44.733) add_atom(model, '222', 1.493, -5.807, 38.239, 44.798) add_atom(model, '223', 1.489, -5.860, 38.205, 44.869) add_atom(model, '224', 1.486, -5.907, 38.169, 44.945) add_atom(model, '225', 1.484, -5.949, 38.132, 45.026) add_atom(model, '226', 1.482, -5.986, 38.095, 45.111) add_atom(model, '227', 1.480, -6.020, 38.060, 45.200) add_atom(model, '228', 1.477, -6.050, 38.028, 45.293) add_atom(model, '229', 1.474, -6.078, 38.000, 45.390) add_atom(model, '230', 1.469, -6.103, 37.976, 45.489) add_atom(model, '231', 1.462, -6.127, 37.959, 45.591) add_atom(model, '232', 1.453, -6.149, 37.946, 45.694) add_atom(model, '233', 1.443, -6.168, 37.937, 45.798) add_atom(model, '234', 1.432, -6.185, 37.931, 45.902) add_atom(model, '235', 1.422, -6.200, 37.929, 46.005) add_atom(model, '236', 1.413, -6.213, 37.928, 46.105) add_atom(model, '237', 1.406, -6.222, 37.929, 46.203) add_atom(model, '238', 1.399, -6.229, 37.930, 46.297) add_atom(model, '239', 1.388, -6.234, 37.931, 46.386) add_atom(model, '240', 1.373, -6.235, 37.931, 46.470) add_atom(model, '241', 1.352, -6.233, 37.932, 46.549) add_atom(model, '242', 1.329, -6.228, 37.935, 46.626) add_atom(model, '243', 1.309, -6.219, 37.941, 46.701) add_atom(model, '244', 1.297, -6.207, 37.952, 46.776) add_atom(model, '245', 1.296, -6.191, 37.969, 46.853) add_atom(model, '246', 1.306, -6.172, 37.994, 46.933) add_atom(model, '247', 1.316, -6.148, 38.029, 47.018) add_atom(model, '248', 1.319, -6.120, 38.075, 47.109) add_atom(model, '249', 1.306, -6.088, 38.133, 47.208) add_atom(model, '250', 1.273, -6.051, 38.203, 47.315) add_atom(model, '251', 1.231, -6.009, 38.281, 47.429) add_atom(model, '252', 1.193, -5.962, 38.363, 47.550) add_atom(model, '253', 1.174, -5.908, 38.446, 47.676) add_atom(model, '254', 1.186, -5.849, 38.526, 47.806) add_atom(model, '255', 1.223, -5.783, 38.597, 47.940) add_atom(model, '256', 1.269, -5.710, 38.658, 48.076) add_atom(model, '257', 1.310, -5.630, 38.702, 48.213) add_atom(model, '258', 1.327, -5.542, 38.728, 48.350) add_atom(model, '259', 1.315, -5.446, 38.730, 48.487) add_atom(model, '260', 1.287, -5.343, 38.711, 48.622) add_atom(model, '261', 1.259, -5.235, 38.673, 48.753) add_atom(model, '262', 1.247, -5.125, 38.621, 48.880) add_atom(model, '263', 1.263, -5.015, 38.559, 49.002) add_atom(model, '264', 1.307, -4.907, 38.490, 49.116) add_atom(model, '265', 1.368, -4.802, 38.417, 49.223) add_atom(model, '266', 1.436, -4.704, 38.345, 49.320) add_atom(model, '267', 1.503, -4.615, 38.277, 49.407) add_atom(model, '268', 1.560, -4.536, 38.217, 49.483) add_atom(model, '269', 1.608, -4.469, 38.167, 49.545) add_atom(model, '270', 1.644, -4.414, 38.126, 49.597) add_atom(model, '271', 1.667, -4.369, 38.094, 49.637) add_atom(model, '272', 1.677, -4.334, 38.068, 49.668) add_atom(model, '273', 1.678, -4.309, 38.048, 49.690) add_atom(model, '274', 1.674, -4.291, 38.032, 49.705) add_atom(model, '275', 1.671, -4.281, 38.018, 49.712) add_atom(model, '276', 1.672, -4.278, 38.006, 49.714) add_atom(model, '277', 1.680, -4.280, 37.995, 49.711) add_atom(model, '278', 1.692, -4.287, 37.982, 49.705) add_atom(model, '279', 1.705, -4.298, 37.968, 49.696) add_atom(model, '280', 1.716, -4.311, 37.954, 49.687) add_atom(model, '281', 1.724, -4.324, 37.942, 49.681) add_atom(model, '282', 1.727, -4.334, 37.931, 49.680) add_atom(model, '283', 1.725, -4.341, 37.924, 49.686) add_atom(model, '284', 1.716, -4.342, 37.921, 49.702) add_atom(model, '285', 1.700, -4.335, 37.923, 49.730) add_atom(model, '286', 1.675, -4.319, 37.932, 49.772) add_atom(model, '287', 1.641, -4.291, 37.947, 49.830) add_atom(model, '288', 1.595, -4.251, 37.971, 49.907) add_atom(model, '289', 1.535, -4.201, 38.002, 50.001) add_atom(model, '290', 1.462, -4.143, 38.039, 50.112) add_atom(model, '291', 1.382, -4.082, 38.080, 50.239) add_atom(model, '292', 1.302, -4.020, 38.125, 50.381) add_atom(model, '293', 1.228, -3.959, 38.172, 50.537) add_atom(model, '294', 1.167, -3.904, 38.220, 50.705) add_atom(model, '295', 1.121, -3.857, 38.268, 50.886) add_atom(model, '296', 1.088, -3.820, 38.315, 51.077) add_atom(model, '297', 1.066, -3.798, 38.359, 51.279) add_atom(model, '298', 1.055, -3.790, 38.401, 51.487) add_atom(model, '299', 1.052, -3.795, 38.439, 51.699) add_atom(model, '300', 1.059, -3.812, 38.476, 51.910) add_atom(model, '301', 1.080, -3.837, 38.510, 52.116) add_atom(model, '302', 1.114, -3.871, 38.542, 52.313) add_atom(model, '303', 1.163, -3.910, 38.573, 52.496) add_atom(model, '304', 1.223, -3.953, 38.603, 52.662) add_atom(model, '305', 1.284, -3.998, 38.632, 52.805) add_atom(model, '306', 1.338, -4.044, 38.660, 52.923) add_atom(model, '307', 1.378, -4.088, 38.688, 53.012) add_atom(model, '308', 1.401, -4.129, 38.716, 53.076) add_atom(model, '309', 1.412, -4.165, 38.746, 53.124) add_atom(model, '310', 1.417, -4.195, 38.777, 53.161) add_atom(model, '311', 1.422, -4.216, 38.812, 53.195) add_atom(model, '312', 1.432, -4.228, 38.850, 53.233) add_atom(model, '313', 1.446, -4.228, 38.892, 53.282) add_atom(model, '314', 1.458, -4.214, 38.940, 53.348) add_atom(model, '315', 1.466, -4.185, 38.993, 53.439) add_atom(model, '316', 1.464, -4.139, 39.053, 53.562) add_atom(model, '317', 1.455, -4.077, 39.120, 53.717) add_atom(model, '318', 1.450, -4.002, 39.191, 53.899) add_atom(model, '319', 1.458, -3.918, 39.264, 54.099) add_atom(model, '320', 1.490, -3.828, 39.337, 54.310) add_atom(model, '321', 1.551, -3.736, 39.408, 54.525) add_atom(model, '322', 1.632, -3.647, 39.475, 54.735) add_atom(model, '323', 1.715, -3.563, 39.535, 54.933) add_atom(model, '324', 1.787, -3.490, 39.586, 55.112) add_atom(model, '325', 1.831, -3.429, 39.626, 55.264) add_atom(model, '326', 1.848, -3.385, 39.653, 55.382) add_atom(model, '327', 1.847, -3.357, 39.668, 55.467) add_atom(model, '328', 1.839, -3.343, 39.673, 55.523) add_atom(model, '329', 1.836, -3.339, 39.671, 55.555) add_atom(model, '330', 1.843, -3.344, 39.663, 55.567) add_atom(model, '331', 1.859, -3.355, 39.652, 55.562) add_atom(model, '332', 1.877, -3.369, 39.639, 55.546) add_atom(model, '333', 1.891, -3.383, 39.627, 55.522) add_atom(model, '334', 1.896, -3.397, 39.618, 55.495) add_atom(model, '335', 1.893, -3.406, 39.614, 55.469) add_atom(model, '336', 1.888, -3.409, 39.616, 55.448) add_atom(model, '337', 1.885, -3.408, 39.621, 55.435) add_atom(model, '338', 1.891, -3.405, 39.626, 55.435) add_atom(model, '339', 1.905, -3.401, 39.629, 55.450) add_atom(model, '340', 1.925, -3.398, 39.626, 55.485) add_atom(model, '341', 1.944, -3.398, 39.614, 55.542) add_atom(model, '342', 1.957, -3.402, 39.592, 55.626) add_atom(model, '343', 1.960, -3.412, 39.555, 55.739) add_atom(model, '344', 1.959, -3.429, 39.501, 55.886) add_atom(model, '345', 1.963, -3.456, 39.427, 56.069) add_atom(model, '346', 1.982, -3.492, 39.335, 56.284) add_atom(model, '347', 2.026, -3.535, 39.230, 56.523) add_atom(model, '348', 2.099, -3.583, 39.116, 56.776) add_atom(model, '349', 2.195, -3.633, 38.997, 57.035) add_atom(model, '350', 2.307, -3.685, 38.878, 57.291) add_atom(model, '351', 2.427, -3.736, 38.765, 57.534) add_atom(model, '352', 2.549, -3.784, 38.660, 57.756) add_atom(model, '353', 2.664, -3.828, 38.570, 57.948) add_atom(model, '354', 2.763, -3.864, 38.497, 58.101) add_atom(model, '355', 2.839, -3.893, 38.446, 58.209) add_atom(model, '356', 2.883, -3.915, 38.415, 58.278) add_atom(model, '357', 2.895, -3.931, 38.399, 58.315) add_atom(model, '358', 2.886, -3.941, 38.396, 58.326) add_atom(model, '359', 2.864, -3.947, 38.404, 58.318) add_atom(model, '360', 2.841, -3.950, 38.418, 58.299) add_atom(model, '361', 2.824, -3.951, 38.435, 58.276) add_atom(model, '362', 2.815, -3.951, 38.454, 58.255) add_atom(model, '363', 2.811, -3.951, 38.470, 58.244) add_atom(model, '364', 2.813, -3.952, 38.480, 58.250) add_atom(model, '365', 2.819, -3.954, 38.484, 58.273) add_atom(model, '366', 2.829, -3.957, 38.483, 58.312) add_atom(model, '367', 2.843, -3.960, 38.478, 58.363) add_atom(model, '368', 2.861, -3.963, 38.471, 58.422) add_atom(model, '369', 2.885, -3.964, 38.464, 58.487) add_atom(model, '370', 2.914, -3.965, 38.457, 58.555) add_atom(model, '371', 2.944, -3.963, 38.452, 58.621) add_atom(model, '372', 2.971, -3.958, 38.450, 58.683) add_atom(model, '373', 2.991, -3.950, 38.453, 58.738) add_atom(model, '374', 3.000, -3.940, 38.462, 58.784) add_atom(model, '375', 3.000, -3.928, 38.476, 58.824) add_atom(model, '376', 2.997, -3.919, 38.493, 58.862) add_atom(model, '377', 2.996, -3.915, 38.513, 58.905) add_atom(model, '378', 3.003, -3.921, 38.535, 58.955) add_atom(model, '379', 3.020, -3.938, 38.557, 59.019) add_atom(model, '380', 3.045, -3.969, 38.578, 59.101) add_atom(model, '381', 3.073, -4.020, 38.596, 59.206) add_atom(model, '382', 3.099, -4.091, 38.611, 59.339) add_atom(model, '383', 3.119, -4.186, 38.622, 59.504) add_atom(model, '384', 3.138, -4.306, 38.627, 59.700) add_atom(model, '385', 3.164, -4.443, 38.629, 59.921) add_atom(model, '386', 3.203, -4.592, 38.628, 60.158) add_atom(model, '387', 3.263, -4.748, 38.626, 60.401) add_atom(model, '388', 3.344, -4.904, 38.623, 60.644) add_atom(model, '389', 3.435, -5.055, 38.620, 60.877) add_atom(model, '390', 3.521, -5.194, 38.620, 61.092) add_atom(model, '391', 3.592, -5.316, 38.622, 61.282) add_atom(model, '392', 3.636, -5.415, 38.629, 61.437) add_atom(model, '393', 3.657, -5.486, 38.640, 61.551) add_atom(model, '394', 3.666, -5.529, 38.654, 61.627) add_atom(model, '395', 3.670, -5.547, 38.669, 61.672) add_atom(model, '396', 3.678, -5.545, 38.680, 61.692) add_atom(model, '397', 3.693, -5.524, 38.685, 61.696) add_atom(model, '398', 3.710, -5.488, 38.682, 61.689) add_atom(model, '399', 3.722, -5.440, 38.667, 61.680) add_atom(model, '400', 3.724, -5.383, 38.636, 61.675) add_atom(model, '401', 3.712, -5.320, 38.588, 61.682) add_atom(model, '402', 3.686, -5.255, 38.520, 61.706) add_atom(model, '403', 3.651, -5.189, 38.430, 61.753) add_atom(model, '404', 3.610, -5.124, 38.323, 61.818) add_atom(model, '405', 3.565, -5.062, 38.204, 61.898) add_atom(model, '406', 3.519, -5.003, 38.077, 61.988) add_atom(model, '407', 3.474, -4.949, 37.948, 62.085) add_atom(model, '408', 3.431, -4.900, 37.820, 62.184) add_atom(model, '409', 3.391, -4.858, 37.699, 62.281) add_atom(model, '410', 3.355, -4.824, 37.589, 62.373) add_atom(model, '411', 3.325, -4.799, 37.495, 62.454) add_atom(model, '412', 3.299, -4.785, 37.421, 62.523) add_atom(model, '413', 3.279, -4.780, 37.367, 62.578) add_atom(model, '414', 3.264, -4.785, 37.329, 62.624) add_atom(model, '415', 3.254, -4.798, 37.305, 62.664) add_atom(model, '416', 3.247, -4.818, 37.290, 62.701) add_atom(model, '417', 3.241, -4.844, 37.283, 62.738) add_atom(model, '418', 3.236, -4.876, 37.278, 62.779) add_atom(model, '419', 3.229, -4.913, 37.274, 62.826) add_atom(model, '420', 3.219, -4.952, 37.266, 62.883) add_atom(model, '421', 3.204, -4.995, 37.252, 62.954) add_atom(model, '422', 3.182, -5.039, 37.229, 63.039) add_atom(model, '423', 3.153, -5.085, 37.196, 63.137) add_atom(model, '424', 3.118, -5.131, 37.155, 63.242) add_atom(model, '425', 3.084, -5.177, 37.104, 63.352) add_atom(model, '426', 3.056, -5.222, 37.045, 63.462) add_atom(model, '427', 3.039, -5.267, 36.976, 63.569) add_atom(model, '428', 3.033, -5.309, 36.900, 63.670) add_atom(model, '429', 3.029, -5.350, 36.814, 63.759) add_atom(model, '430', 3.020, -5.387, 36.721, 63.834) add_atom(model, '431', 2.994, -5.421, 36.619, 63.891) add_atom(model, '432', 2.946, -5.452, 36.510, 63.930) add_atom(model, '433', 2.878, -5.479, 36.394, 63.952) add_atom(model, '434', 2.797, -5.504, 36.272, 63.959) add_atom(model, '435', 2.711, -5.526, 36.145, 63.954) add_atom(model, '436', 2.626, -5.547, 36.013, 63.939) add_atom(model, '437', 2.545, -5.566, 35.878, 63.915) add_atom(model, '438', 2.469, -5.583, 35.741, 63.885) add_atom(model, '439', 2.395, -5.600, 35.602, 63.851) add_atom(model, '440', 2.322, -5.617, 35.462, 63.815) for a in range(len(model.atom) - 1): b = chempy.Bond() b.index = [a, a + 1] model.bond.append(b) cmd.set('surface_mode', 1) cmd.set('sphere_mode', 9) cmd.set('mesh_mode', 1) cmd.load_model(model, 'channel4') cmd.hide('everything', 'channel4') cmd.set('sphere_color', 'yellow', 'channel4') cmd.show('spheres', 'channel4') channel4() cmd.group('Channels', [channel4], 'add')